Structured Review

Illumina Inc hiseq2000
Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a <t>HiSeq2000</t> sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.
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1) Product Images from "Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems"

Article Title: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

Journal: Genome Biology

doi: 10.1186/gb-2011-12-11-r112

Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.
Figure Legend Snippet: Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.

Techniques Used: Sequencing

2) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

3) Product Images from "Sequencing-based high throughput mutation detection in bread wheat"

Article Title: Sequencing-based high throughput mutation detection in bread wheat

Journal: BMC Genomics

doi: 10.1186/s12864-015-2112-1

Schematic diagram for mutation detection using novel application of Genotyping-by-sequencing (GBS). a DNA of 24 plants including 22 EMS generated M2 and two wild types was digested with Ape KI followed by unique barcode (highlighted in orange , cyan , purple , and green ) and common adapter (highlighted in red ) ligation. All samples were pooled together before PCR amplification. Pooled sample library was evaluated for its quality and size. Sequencing of the library was performed on Illumina HiSeq2000. b Raw data files processed according to the filters described in Methods section. Differentiation of EMS SNPs from homoeologous SNPs is shown from three mutant plants where homoeologous SNP positions are marked in red and blue while mutational SNPs are highlighted in purple
Figure Legend Snippet: Schematic diagram for mutation detection using novel application of Genotyping-by-sequencing (GBS). a DNA of 24 plants including 22 EMS generated M2 and two wild types was digested with Ape KI followed by unique barcode (highlighted in orange , cyan , purple , and green ) and common adapter (highlighted in red ) ligation. All samples were pooled together before PCR amplification. Pooled sample library was evaluated for its quality and size. Sequencing of the library was performed on Illumina HiSeq2000. b Raw data files processed according to the filters described in Methods section. Differentiation of EMS SNPs from homoeologous SNPs is shown from three mutant plants where homoeologous SNP positions are marked in red and blue while mutational SNPs are highlighted in purple

Techniques Used: Mutagenesis, Sequencing, Generated, Ligation, Polymerase Chain Reaction, Amplification

4) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

5) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

6) Product Images from "ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing"

Article Title: ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2012.03.002

Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)
Figure Legend Snippet: Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)

Techniques Used:

7) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

8) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

9) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

10) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

11) Product Images from "EST sequencing and gene expression profiling in Scutellaria baicalensis"

Article Title: EST sequencing and gene expression profiling in Scutellaria baicalensis

Journal: EXCLI Journal

doi:

Summary of sequencing data derived from the GS_FLX+ and HiSeq2000 platforms
Figure Legend Snippet: Summary of sequencing data derived from the GS_FLX+ and HiSeq2000 platforms

Techniques Used: Sequencing, Derivative Assay

12) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

13) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

14) Product Images from "ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing"

Article Title: ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2012.03.002

Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)
Figure Legend Snippet: Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)

Techniques Used:

15) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

16) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

17) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

18) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

19) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

20) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

21) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

22) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

23) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

24) Product Images from "SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing"

Article Title: SNP Discovery in European Anchovy (Engraulis encrasicolus, L) by High-Throughput Transcriptome and Genome Sequencing

Journal: PLoS ONE

doi: 10.1371/journal.pone.0070051

Map with sampling locations. Stars indicate sample locations used for 454 GS FLX and HiSeq2000 sequencing: 1 (BIS2; N = 2) and 2 (BIS1; N = 3) represent sampling points from Bay of Biscay population, 3 (TAR; N = 2) is the sampling point from Mediterranean population and 4 (CAD; N = 3) is the sample from the Atlantic population. Every sampling point (stars and black dots) was used for validation including N = 30 individuals. Apart from locations 1–4, two additional populations were included in this step: 5 (CAN) is the sampling location for Canary Islands population and 6 (NOR) is the sample representing North Sea population.
Figure Legend Snippet: Map with sampling locations. Stars indicate sample locations used for 454 GS FLX and HiSeq2000 sequencing: 1 (BIS2; N = 2) and 2 (BIS1; N = 3) represent sampling points from Bay of Biscay population, 3 (TAR; N = 2) is the sampling point from Mediterranean population and 4 (CAD; N = 3) is the sample from the Atlantic population. Every sampling point (stars and black dots) was used for validation including N = 30 individuals. Apart from locations 1–4, two additional populations were included in this step: 5 (CAN) is the sampling location for Canary Islands population and 6 (NOR) is the sample representing North Sea population.

Techniques Used: Sampling, Sequencing

25) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

26) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

27) Product Images from "A Comprehensive Analysis of the T and B Lymphocytes Repertoire Shaped by HIV Vaccines"

Article Title: A Comprehensive Analysis of the T and B Lymphocytes Repertoire Shaped by HIV Vaccines

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2018.02194

Schema of the work flow used in this study. Eighteen (18) rhesus macaques were divided equally into three groups (5-Helix, N51. and N36) (total 54 samples) and administered with the corresponding vaccines. The vaccination regimen contains the preliminary series of vaccination and the boost vaccination. The 18 macaques were sampled for the first time at Day 0 prior boost. After the boost, the macaques were further sampled at day 7 and 10. Both T and B cell repertoires of the 54 samples were captured, and prepared into 108 sequencing libraries for Illumina Hiseq2000. Raw sequencing data were then subjected to IMonitor work flow for basic TCR and IGH repertoire analysis.
Figure Legend Snippet: Schema of the work flow used in this study. Eighteen (18) rhesus macaques were divided equally into three groups (5-Helix, N51. and N36) (total 54 samples) and administered with the corresponding vaccines. The vaccination regimen contains the preliminary series of vaccination and the boost vaccination. The 18 macaques were sampled for the first time at Day 0 prior boost. After the boost, the macaques were further sampled at day 7 and 10. Both T and B cell repertoires of the 54 samples were captured, and prepared into 108 sequencing libraries for Illumina Hiseq2000. Raw sequencing data were then subjected to IMonitor work flow for basic TCR and IGH repertoire analysis.

Techniques Used: Flow Cytometry, Sequencing

28) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

29) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

30) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

31) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

32) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

33) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

34) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

35) Product Images from "ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing"

Article Title: ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing

Journal: The Journal of Molecular Diagnostics : JMD

doi: 10.1016/j.jmoldx.2012.03.002

Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)
Figure Legend Snippet: Depth of coverage. Depth of coverage from a representative patient sample run on a single lane of a HiSeq2000 instrument in a 96 - plexed ColoSeq run. A: Distribution of coverage for each targeted base. Each bar represents the number of base pairs (in 1000s)

Techniques Used:

36) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

37) Product Images from "Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies"

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

Journal: PLoS ONE

doi: 10.1371/journal.pone.0066621

Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.
Figure Legend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

Techniques Used: Standard Deviation

GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.
Figure Legend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

Techniques Used:

38) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

39) Product Images from "Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms"

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms

Journal: Scientific Reports

doi: 10.1038/s41598-018-23325-2

GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: GC plots for HiSeq2000 ( a ) and Proton ( b ) platforms. A heat map describes rates for each (GC, Original copy ratio) pair. Smoothed loess curves (black line) are fitted to represent the local original copy ratio trend. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: CNV detection on HiSeq2000 ( a ) and Proton ( b ) platforms. FNR is short for false negative rate which equal to the false negative signal number divided by the total true positive signal number. FPR is short for false positive rate which equal to the signal number divided by the total true positive signal number. TNR is short for negative true negative rate which equal to the true negative signal number divided by the total true negative signal number. TPR is short for true positive rate which equal to the true positive signal number divided by the total true positive signal number. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Distribution of NDR values for the four combinations across the whole genome on HiSeq2000 ( a ) and Proton ( b ) platforms. Box plot represents NDR values in 124,011 windows for the same sample. x-axis is Chromosome number; y-axis is NDR values. The left and right represent the comparison without GC-correction and after GC-correction, respectively, for the same combination. The CV is the coefficient of variation of NDR across the whole genome. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Values of ΔR GC for the four combinations between Hiseq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.
Figure Legend Snippet: Reproducibility of the four combinations between HiSeq2000 and Proton platforms. The box-plot represents the correlation of 11 cell lines used in this study for HiSeq2000 and Proton platforms. RS, RM, SS, SM are four combinations. RS is short for Rubicon PicoPLEX WGA Kit and single cell, RM is short for Rubicon PicoPLEX WGA Kit and multiple cells, SS is short for Sigma-Aldrich WGA4 kit and single cell, SM is short for Sigma-Aldrich WGA4 kit and multiple cells.

Techniques Used: Whole Genome Amplification

40) Product Images from "ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING"

Article Title: ENABLING CLINICAL CANCER GENOMICS FOR RARE MUTATIONS: COLD-PCR MAGNIFIES MUTATIONS PRIOR TO TARGETED AMPLICON RE-SEQUENCING

Journal: Clinical chemistry

doi: 10.1373/clinchem.2011.176198

Mutation Detection via Targeted Amplicon Resequencing on the Illumina HiSeq2000: Clinical specimens
Figure Legend Snippet: Mutation Detection via Targeted Amplicon Resequencing on the Illumina HiSeq2000: Clinical specimens

Techniques Used: Mutagenesis, Amplification

Related Articles

Sequencing:

Article Title: ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing
Article Snippet: .. However, an important drawback of these more rapid instruments is that only about 1 to 2 Gb of sequence data are generated per run, compared with 30 to 40 Gb for a single lane of a HiSeq2000. .. We estimate that only about three to five index barcoded samples could be pooled per run on the MiSeq using 100-bp or 150-bp paired-end reads to achieve the same depth of coverage as our current 96-plexed assay on the HiSeq2000.

Article Title: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
Article Snippet: .. The HiSeq2000 became commercially available in the second quarter of 2010 and uses sequencing-by-synthesis (SBS) chemistry similar to the Illumina GA series but at a two- to five-fold increased rate of data acquisition. .. A HiSeq flow cell can be imaged on both the top and bottom surface.

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. DNA sequencing and data processing Paired-end sequencing (100 bp reads) was performed on a single flowcell channel of HiSeq2000 (Illumina, Inc., San Diego, CA). ..

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: .. The HiSeq2000 (Illumina, San Diego, CA, US) exploits highly parallel optical sensing of polymerization reactions and sequencing-by-synthesis technology to implement ultra-high throughput sequencing, although the procedure requires long turnaround time (TAT) . .. For the other platform, Life Technologies released an integrated semiconductor sequencing device, Ion Proton (Thermo Fisher Scientific, Waltham, MA, USA), which is reported to provide shorter TAT and a more cost-effective NGS solution than those of alternative platforms .

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: .. In conclusion, the WGA4 kit had better uniformity than that of PicoPLEX WGA Kit on both Hiseq2000 and Ion Proton sequencing platforms. .. With expectations, the CV value of multiple cells was lower than that of single cell independent of WGA kit and sequencing platforms.

Generated:

Article Title: ColoSeq Provides Comprehensive Lynch and Polyposis Syndrome Mutational Analysis Using Massively Parallel Sequencing
Article Snippet: .. However, an important drawback of these more rapid instruments is that only about 1 to 2 Gb of sequence data are generated per run, compared with 30 to 40 Gb for a single lane of a HiSeq2000. .. We estimate that only about three to five index barcoded samples could be pooled per run on the MiSeq using 100-bp or 150-bp paired-end reads to achieve the same depth of coverage as our current 96-plexed assay on the HiSeq2000.

other:

Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies
Article Snippet: Interestingly, for not correctly called homozygous SNPs by HiSeq2000 the number of no-calls on one allele is approximately in the same range as for those not being called on both alleles ( ).

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: On HiSeq2000, the CV values were 0.31 ± 0.01 in RM, 0.29 ± 0.02 in SM, 0.39 ± 0.14 in RS and 0.40 ± 0.06 in SS.

Whole Genome Amplification:

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: .. Furthermore, the ErrorRate of Hiseq2000 was lower than that of Ion Proton with the same WGA kit. .. However, whether the map rate of Ion Proton was higher than that of Hiseq2000 or the difference between the mismatch rate, insertion rate and deletion rate was significant could not be determined because the two sequencing platforms were not comparable because of the different alignment methods used and different sequencing principles .

Article Title: Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
Article Snippet: .. In conclusion, the WGA4 kit had better uniformity than that of PicoPLEX WGA Kit on both Hiseq2000 and Ion Proton sequencing platforms. .. With expectations, the CV value of multiple cells was lower than that of single cell independent of WGA kit and sequencing platforms.

DNA Sequencing:

Article Title: Sequencing-based high throughput mutation detection in bread wheat
Article Snippet: .. DNA sequencing and data processing Paired-end sequencing (100 bp reads) was performed on a single flowcell channel of HiSeq2000 (Illumina, Inc., San Diego, CA). ..

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    Illumina Inc illumina hiseq2000
    Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The <t>Illumina</t> <t>HiSeq2000</t> platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).
    Illumina Hiseq2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 599 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc illumina hiseq2000 sequencing
    The circulating miRNAs signatures identified by <t>Illumina</t> <t>Hiseq2000</t> sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).
    Illumina Hiseq2000 Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).

    Journal: BMC Genomics

    Article Title: A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses

    doi: 10.1186/1471-2164-13-99

    Figure Lengend Snippet: Overview of the reference transcriptome sequencing, and result of the Velvet/Oases assembly . A) RNA for the reference was pooled from all of the test samples. The Illumina HiSeq2000 platform was used to generate data for de novo assembly including large transcripts (LT) equivalent to 15,493 potential protein coding sequences. B) The accuracy and integrity of the assembly was assessed by BLAST comparison (100 bp overlap and ≥ 98% sequence identity) with the publicly available collection of sugar beet ESTs at the Sugar Beet Gene Index (SBGI), hosted at the Dana Farber Cancer Institute (DFCI).

    Article Snippet: Digital gene expression profiling and mapping to reference cDNA libraries generated from sub-samples of each test sample were sequenced (Illumina HiSeq2000, 50 bp single read module).

    Techniques: Sequencing

    Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Journal: Scientific Data

    Article Title: De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris

    doi: 10.1038/sdata.2016.83

    Figure Lengend Snippet: Schematic overview of the study. We collected one sample for each tissue type, including root, stem, leaf, flower bud, column, lip, petal, sepal and seeds from three developmental stages of P. equestris . Next, we sequenced cDNAs generated from the tissues on an Illumina HiSeq2000 in 90-bp paired-end (PE) reads, with 75-bp paired-end (PE) reads from the leaf tissue. The analysis started with assembling the short reads using the de novo assembly program Trinity and continued with functional analysis using BLASTX. Moreover, we performed quality control assessments at each step from the raw reads to the annotation datasets. Finally, we used YABBY and NBS-encoding gene families as examples of the usage of these datasets.

    Article Snippet: After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris , we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds.

    Techniques: Generated, Functional Assay

    The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Journal: Scientific Reports

    Article Title: The plasma miR-125a, miR-361 and miR-133a are promising novel biomarkers for Late-Onset Hypogonadism

    doi: 10.1038/srep23531

    Figure Lengend Snippet: The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Article Snippet: Using Illumina HiSeq2000 sequencing at discovery phase, and then two-step validated by reverse transcriptase polymerase chain reaction (RT-PCR) assays in verification phases.

    Techniques: Sequencing