illumina hiseq x  (Illumina Inc)

 
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    Name:
    HiSeq X Installation and Operational Qualification
    Description:
    Comprehensive Qualification Services from Illumina Illumina Installation and Operational Qualification IQ OQ services carry out numerous experiments for each system to ensure critical components are tested and validated have cut off metrics and to confirm these metrics show the system is operating in accordance with specifications Our IQ service provides documented verification that instrument is installed according to our specifications and safety regulations During the IQ a trained engineer verifies latest supported firmware and software versions were installed verifies instrument setup and accessory logistics checks physical and environmental safety conditions are met and provides a signed audit ready report Our OQ service follows a comprehensive well defined protocol to verify the system functions according to pre set and validated operational specifications We update the OQ protocol following each instrument hardware and software release ensuring your laboratory receives the most up to date service Critical aspects of the OQ include motion qualification optics qualification fluidics qualification and thermal qualification As regulatory guidelines continue to evolve and increase in stringency laboratories need well documented system qualification protocols for compliance Performed by Illumina trained and certified engineers IQ OQ helps research and diagnostic genomic laboratories meet regulatory guidelines Provides an audit ready signed IQ OQ report Accelerates use by ensuring the Illumina instrument is installed operational and ready to use after initial delivery Verifies Illumina sequencers perform according to manufacturer specifications after major repairs relocation or system software upgrades Helps establish instrument log files for change control Provides engineer training and tool calibration certificates upon customer request
    Catalog Number:
    sp-102-1106
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    Service Products
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    Structured Review

    Illumina Inc illumina hiseq x
    HiSeq X Installation and Operational Qualification
    Comprehensive Qualification Services from Illumina Illumina Installation and Operational Qualification IQ OQ services carry out numerous experiments for each system to ensure critical components are tested and validated have cut off metrics and to confirm these metrics show the system is operating in accordance with specifications Our IQ service provides documented verification that instrument is installed according to our specifications and safety regulations During the IQ a trained engineer verifies latest supported firmware and software versions were installed verifies instrument setup and accessory logistics checks physical and environmental safety conditions are met and provides a signed audit ready report Our OQ service follows a comprehensive well defined protocol to verify the system functions according to pre set and validated operational specifications We update the OQ protocol following each instrument hardware and software release ensuring your laboratory receives the most up to date service Critical aspects of the OQ include motion qualification optics qualification fluidics qualification and thermal qualification As regulatory guidelines continue to evolve and increase in stringency laboratories need well documented system qualification protocols for compliance Performed by Illumina trained and certified engineers IQ OQ helps research and diagnostic genomic laboratories meet regulatory guidelines Provides an audit ready signed IQ OQ report Accelerates use by ensuring the Illumina instrument is installed operational and ready to use after initial delivery Verifies Illumina sequencers perform according to manufacturer specifications after major repairs relocation or system software upgrades Helps establish instrument log files for change control Provides engineer training and tool calibration certificates upon customer request
    https://www.bioz.com/result/illumina hiseq x/product/Illumina Inc
    Average 99 stars, based on 875 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq x - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing"

    Article Title: Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0190264

    The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).
    Figure Legend Snippet: The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).

    Techniques Used: Sequencing

    2) Product Images from "A synthetic-diploid benchmark for accurate variant calling evaluation"

    Article Title: A synthetic-diploid benchmark for accurate variant calling evaluation

    Journal: Nature methods

    doi: 10.1038/s41592-018-0054-7

    Evaluating variant calling accuracy with Syndip. %FNR denotes percent false negative rate, and FPPM is the number of false positives per million bases. (a) Comparison of Syndip, GIAB and PlatGen benchmark datasets on filtered calls. For GIAB and PlatGen, variants were called from the HiSeq X Ten run ‘NA12878_L7_S7’ available from the Illumina BaseSpace. (b) Effect of evaluation regions. Low-complexity regions were identified with the symmetric DUST algorithm. The ‘hard-to-call’ regions include low-complexity regions, regions unmappable with 75bp single-end reads and regions susceptible to common copy number variations. Panels (c)–(f) only show metrics in ‘coding+conserved’ regions. (c) Effect of variant filters. Green bars applied Platypus built-in filters. (d) Effect of the human genome reference build. Decoy sequences 17 are real human sequences that are missing from GRCh37. (e) Effect of the mapping algorithms and post-processing. BWA-MEM* represents alignment post-processed with base quality recalibration and INDEL realignment; other alignments were not processed with these steps. (f) Effect of replicates. Replicate 1–4 were sequenced from four independent libraries, respectively, by mixing equal amount of DNA prior to library construction. Replicate 5* was generated by computationally subsampling and mixing reads sequenced from the two CHM cell lines separately. Replicate 1 is used in panels (a)–(e). Numerical data and the script to generate the figure are available as Supplementary Data .
    Figure Legend Snippet: Evaluating variant calling accuracy with Syndip. %FNR denotes percent false negative rate, and FPPM is the number of false positives per million bases. (a) Comparison of Syndip, GIAB and PlatGen benchmark datasets on filtered calls. For GIAB and PlatGen, variants were called from the HiSeq X Ten run ‘NA12878_L7_S7’ available from the Illumina BaseSpace. (b) Effect of evaluation regions. Low-complexity regions were identified with the symmetric DUST algorithm. The ‘hard-to-call’ regions include low-complexity regions, regions unmappable with 75bp single-end reads and regions susceptible to common copy number variations. Panels (c)–(f) only show metrics in ‘coding+conserved’ regions. (c) Effect of variant filters. Green bars applied Platypus built-in filters. (d) Effect of the human genome reference build. Decoy sequences 17 are real human sequences that are missing from GRCh37. (e) Effect of the mapping algorithms and post-processing. BWA-MEM* represents alignment post-processed with base quality recalibration and INDEL realignment; other alignments were not processed with these steps. (f) Effect of replicates. Replicate 1–4 were sequenced from four independent libraries, respectively, by mixing equal amount of DNA prior to library construction. Replicate 5* was generated by computationally subsampling and mixing reads sequenced from the two CHM cell lines separately. Replicate 1 is used in panels (a)–(e). Numerical data and the script to generate the figure are available as Supplementary Data .

    Techniques Used: Variant Assay, Generated

    3) Product Images from "Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes"

    Article Title: Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

    Journal: G3: Genes|Genomes|Genetics

    doi: 10.1534/g3.118.200481

    Samples for the transcriptomics-assisted genetic variant identification of some key genes involved in nitrogen use efficiency regulating in Brassica napus . Transctiptional expression profiling, gene co-expression network analysis and genetic variants of BnaNRT1.1s (A), BnaNRT2.1s (B), BnaNRT1.5s (C) and BnaNRT1.8s (D). For RNA sequencing, the rapeseed seedlings were cultivated under high NO 3 - (6.0 mM) for 10 d, and then transferred to low NO 3 - (0.30 mM). At 0 h, 3 h and 72 h, the shoots and roots of the seedlings were individually sampled with three independent biological replicates. RNA-seq was performed on an Illumina Hiseq X Ten platform (Illumina Inc., San Diego, CA, USA), which generated approximate 6.0-Gb of sequencing data with 150-bp paired-end (PE) reads for each sample. Transcript abundances (FPKM values) were determined from the RNA-seq data with the method described by Hua et al. (2017) . For the gene co-expression network performed by CYTOSCAPE v. 3.2.1, cycle nodes represent genes, and the size of the nodes represents the power of the interrelation among the nodes by degree value. Edges between two nodes represent interactions between genes.
    Figure Legend Snippet: Samples for the transcriptomics-assisted genetic variant identification of some key genes involved in nitrogen use efficiency regulating in Brassica napus . Transctiptional expression profiling, gene co-expression network analysis and genetic variants of BnaNRT1.1s (A), BnaNRT2.1s (B), BnaNRT1.5s (C) and BnaNRT1.8s (D). For RNA sequencing, the rapeseed seedlings were cultivated under high NO 3 - (6.0 mM) for 10 d, and then transferred to low NO 3 - (0.30 mM). At 0 h, 3 h and 72 h, the shoots and roots of the seedlings were individually sampled with three independent biological replicates. RNA-seq was performed on an Illumina Hiseq X Ten platform (Illumina Inc., San Diego, CA, USA), which generated approximate 6.0-Gb of sequencing data with 150-bp paired-end (PE) reads for each sample. Transcript abundances (FPKM values) were determined from the RNA-seq data with the method described by Hua et al. (2017) . For the gene co-expression network performed by CYTOSCAPE v. 3.2.1, cycle nodes represent genes, and the size of the nodes represents the power of the interrelation among the nodes by degree value. Edges between two nodes represent interactions between genes.

    Techniques Used: Variant Assay, Expressing, RNA Sequencing Assay, Generated, Sequencing

    4) Product Images from "Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing"

    Article Title: Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0190264

    The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).
    Figure Legend Snippet: The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).

    Techniques Used: Sequencing

    Related Articles

    Sequencing:

    Article Title: Direct determination of diploid genome sequences
    Article Snippet: .. Sequencing was conducted with an Illumina HiSeq X with 2x150 paired-end reads based on manufacturer's protocols. .. Internal representation of Supernova assembliesAn assembly is first represented as a directed graph in which each edge represents a single strand of DNA sequence.

    Article Title: SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples
    Article Snippet: .. Paired-End 150 sequencing was performed using the HiSeq X Ten platform (Illumina, San Diego, CA) supporting dual indexing with raw sequencing depths over 20,000×. .. Duplex consensus sequence generation The complete computational workflow of the SinoDuplex approach is illustrated in .

    Article Title: First de novo whole genome sequencing and assembly of the bar-headed goose
    Article Snippet: .. De novo sequencing was conducted with an Illumina HiSeq X Ten platform. ..

    Construct:

    Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
    Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

    Purification:

    Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
    Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

    cDNA Library Assay:

    Article Title: Coordinated mechanisms of leaves and roots in response to drought stress underlying full-length transcriptome profiling in Vicia sativa L
    Article Snippet: .. The cDNA library was sequenced with a 100-bp paired-end format using the Illumina HiSeq X Ten, and each sample yielded more than 6 Gb of clean data. ..

    Polymerase Chain Reaction:

    Article Title: C-KIT Expression Distinguishes Fetal from Postnatal Skeletal Progenitors
    Article Snippet: .. PCR products were purified with AMPure XP beads (Agencourt) and quantified with a Qubit dsDNA HS Assay Kit (Thermo Fisher). cDNA libraries were constructed with a Nextera XT DNA Library Preparation Kit (Illumina) and were sequenced on an Illumina HiSeq X Ten instrument in 150-bp paired-end-read mode by Berry Genomics. .. The amplification, cDNA purification, and library construction were performed on the Agilent Bravo automatic liquid-handling platform in the core facility for molecular biology at SIBCB.

    ChIP-sequencing:

    Article Title: Tandem Directional CTCF Sites Balance Protocadherin Promoter Usage
    Article Snippet: .. ChIP-seq libraries were sequenced on a HiSeq X Ten Platform (Illumina). .. Quantitative High-resolution Chromatin Conformation Capture Copy (QHR-4C)The QHR-4C protocol was modified from previously published method [ ].

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    Illumina Inc hiseq x
    Coverage comparison between HiSeq 2500 and <t>HiSeq</t> X Ten. a Plot shows the fraction of genome covered at different depths for four samples sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. The coverage plot for the HiSeq 2500 HO mode is the merged coverage obtained from multiplexing the four samples. b Plot shows the fraction of CpG sites covered at different depths when four clinical samples are sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. c , d Box plot showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a sample sequenced on one lane of HiSeq X Ten ( c ) and HiSeq 2500 ( d )
    Hiseq X, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 188 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq x/product/Illumina Inc
    Average 99 stars, based on 188 article reviews
    Price from $9.99 to $1999.99
    hiseq x - by Bioz Stars, 2020-09
    99/100 stars
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    99
    Illumina Inc illumina hiseq x
    The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in <t>Illumina</t> for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the <t>HiSeq</t> X Ten or BGISEQ-500 data is plotted ( c ).
    Illumina Hiseq X, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 875 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq x/product/Illumina Inc
    Average 99 stars, based on 875 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq x - by Bioz Stars, 2020-09
    99/100 stars
      Buy from Supplier

    Image Search Results


    Coverage comparison between HiSeq 2500 and HiSeq X Ten. a Plot shows the fraction of genome covered at different depths for four samples sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. The coverage plot for the HiSeq 2500 HO mode is the merged coverage obtained from multiplexing the four samples. b Plot shows the fraction of CpG sites covered at different depths when four clinical samples are sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. c , d Box plot showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a sample sequenced on one lane of HiSeq X Ten ( c ) and HiSeq 2500 ( d )

    Journal: Epigenetics & Chromatin

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    doi: 10.1186/s13072-018-0194-0

    Figure Lengend Snippet: Coverage comparison between HiSeq 2500 and HiSeq X Ten. a Plot shows the fraction of genome covered at different depths for four samples sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. The coverage plot for the HiSeq 2500 HO mode is the merged coverage obtained from multiplexing the four samples. b Plot shows the fraction of CpG sites covered at different depths when four clinical samples are sequenced together on one lane of the HiSeq 2500 versus when each of the samples is sequenced on a single lane of the HiSeq X Ten. c , d Box plot showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a sample sequenced on one lane of HiSeq X Ten ( c ) and HiSeq 2500 ( d )

    Article Snippet: Comparison of overall methylation correlation for intact genomic DNA and FFPET between HiSeq 2500 and HiSeq X Ten We observed that despite differences in the chemistry between the two Illumina sequencing platforms and resulting genome-wide coverage per lane of sequencing, there is a remarkable correlation between the methylation calls obtained from the HiSeq 2500 and HiSeq X Ten, as demonstrated using DNA from a cell line, clinical sample and FFPET sample (Pearson r > 0.94) (Fig. a).

    Techniques: Multiplexing

    Comparison of methylation correlation between HiSeq 2500 and HiSeq X Ten. a Correlation plots of methylation levels obtained from a cell line, a clinical sample and a FFPET sample sequenced on the Hiseq 2500 versus HiSeq X Ten (Pearson r > 0.94). b Correlation of methylation values obtained from HiSeq 2500 and HiSeq X Ten for a cell line, clinical sample and a FFPET sample after grouping them into four bins of methylation percentages. c Average kappa values for six sample pairs, including two cell lines, two clinical samples and two FFPE samples compared between the HiSeq 2500 and HiSeq X Ten platform. d Bar plot showing the distribution of percentage of discordant sites across the genome for a cell line, clinical sample and a FFPET sample

    Journal: Epigenetics & Chromatin

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    doi: 10.1186/s13072-018-0194-0

    Figure Lengend Snippet: Comparison of methylation correlation between HiSeq 2500 and HiSeq X Ten. a Correlation plots of methylation levels obtained from a cell line, a clinical sample and a FFPET sample sequenced on the Hiseq 2500 versus HiSeq X Ten (Pearson r > 0.94). b Correlation of methylation values obtained from HiSeq 2500 and HiSeq X Ten for a cell line, clinical sample and a FFPET sample after grouping them into four bins of methylation percentages. c Average kappa values for six sample pairs, including two cell lines, two clinical samples and two FFPE samples compared between the HiSeq 2500 and HiSeq X Ten platform. d Bar plot showing the distribution of percentage of discordant sites across the genome for a cell line, clinical sample and a FFPET sample

    Article Snippet: Comparison of overall methylation correlation for intact genomic DNA and FFPET between HiSeq 2500 and HiSeq X Ten We observed that despite differences in the chemistry between the two Illumina sequencing platforms and resulting genome-wide coverage per lane of sequencing, there is a remarkable correlation between the methylation calls obtained from the HiSeq 2500 and HiSeq X Ten, as demonstrated using DNA from a cell line, clinical sample and FFPET sample (Pearson r > 0.94) (Fig. a).

    Techniques: Methylation, Formalin-fixed Paraffin-Embedded

    Difference in HiSeq X Ten coverage distribution for FFPET bisulphite library prepared from two methods. a , b Box plot showing the difference in coverage across CpG islands, CpG shores and other regions of the genome for TruMethyl WG ( a ) and Accel-NGS Methyl-Seq ( b ) methods, when sequenced on the HiSeq X Ten. c IGV plot showing the difference in distribution of reads for a FFPET library obtained from the TruMethyl WG method and Accel-NGS Methyl-Seq method across a CpG island. d , e Box plots showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a FFPET library prepared by the TruMethyl WG ( d ) and Accel-NGS Methyl-Seq ( e ) methods and sequenced on one lane of HiSeq X Ten

    Journal: Epigenetics & Chromatin

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    doi: 10.1186/s13072-018-0194-0

    Figure Lengend Snippet: Difference in HiSeq X Ten coverage distribution for FFPET bisulphite library prepared from two methods. a , b Box plot showing the difference in coverage across CpG islands, CpG shores and other regions of the genome for TruMethyl WG ( a ) and Accel-NGS Methyl-Seq ( b ) methods, when sequenced on the HiSeq X Ten. c IGV plot showing the difference in distribution of reads for a FFPET library obtained from the TruMethyl WG method and Accel-NGS Methyl-Seq method across a CpG island. d , e Box plots showing the coverage distribution across exons, intergenic regions, introns, promoter regions and repeat regions of the genome for a FFPET library prepared by the TruMethyl WG ( d ) and Accel-NGS Methyl-Seq ( e ) methods and sequenced on one lane of HiSeq X Ten

    Article Snippet: Comparison of overall methylation correlation for intact genomic DNA and FFPET between HiSeq 2500 and HiSeq X Ten We observed that despite differences in the chemistry between the two Illumina sequencing platforms and resulting genome-wide coverage per lane of sequencing, there is a remarkable correlation between the methylation calls obtained from the HiSeq 2500 and HiSeq X Ten, as demonstrated using DNA from a cell line, clinical sample and FFPET sample (Pearson r > 0.94) (Fig. a).

    Techniques: Next-Generation Sequencing

    Correlation between duplicate reads, spike-ins and the sequencing platforms. a , b Plots showing the frequency of distribution of duplicate reads for two cell line DNA samples during down sampling of the raw reads from HiSeq X Ten to the number of raw reads obtained from HiSeq 2500. c Box plot showing the difference in duplicate percentage when the same set of ten bisulphite libraries were spiked with 25% of 250 pM genomic library and 25% of 300 pM PhiX library

    Journal: Epigenetics & Chromatin

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    doi: 10.1186/s13072-018-0194-0

    Figure Lengend Snippet: Correlation between duplicate reads, spike-ins and the sequencing platforms. a , b Plots showing the frequency of distribution of duplicate reads for two cell line DNA samples during down sampling of the raw reads from HiSeq X Ten to the number of raw reads obtained from HiSeq 2500. c Box plot showing the difference in duplicate percentage when the same set of ten bisulphite libraries were spiked with 25% of 250 pM genomic library and 25% of 300 pM PhiX library

    Article Snippet: Comparison of overall methylation correlation for intact genomic DNA and FFPET between HiSeq 2500 and HiSeq X Ten We observed that despite differences in the chemistry between the two Illumina sequencing platforms and resulting genome-wide coverage per lane of sequencing, there is a remarkable correlation between the methylation calls obtained from the HiSeq 2500 and HiSeq X Ten, as demonstrated using DNA from a cell line, clinical sample and FFPET sample (Pearson r > 0.94) (Fig. a).

    Techniques: Sequencing, Sampling

    Integrating whole genome and whole genome bisulphite sequencing. a Bar plot depicting the coverage obtained when both genomic and its corresponding bisulphite library is sequenced on the same lane of the HiSeq X Ten, for four prostate cancer samples sequenced in duplicate ( a , b ). b A representative IGV plot showing a C to T SNP identified in both the WGS and WGBS data at approximately 13× coverage. c Bar plot indicating the percentage of SNPs from WGBS concordant in spike-in WGS at 13× and 26× coverage. d A representative Venn diagram for one prostate cancer sample, 2a showing the number of SNPs concordant and discordant at 13× and 26× coverage for both WGBS and spike-in WGS

    Journal: Epigenetics & Chromatin

    Article Title: Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

    doi: 10.1186/s13072-018-0194-0

    Figure Lengend Snippet: Integrating whole genome and whole genome bisulphite sequencing. a Bar plot depicting the coverage obtained when both genomic and its corresponding bisulphite library is sequenced on the same lane of the HiSeq X Ten, for four prostate cancer samples sequenced in duplicate ( a , b ). b A representative IGV plot showing a C to T SNP identified in both the WGS and WGBS data at approximately 13× coverage. c Bar plot indicating the percentage of SNPs from WGBS concordant in spike-in WGS at 13× and 26× coverage. d A representative Venn diagram for one prostate cancer sample, 2a showing the number of SNPs concordant and discordant at 13× and 26× coverage for both WGBS and spike-in WGS

    Article Snippet: Comparison of overall methylation correlation for intact genomic DNA and FFPET between HiSeq 2500 and HiSeq X Ten We observed that despite differences in the chemistry between the two Illumina sequencing platforms and resulting genome-wide coverage per lane of sequencing, there is a remarkable correlation between the methylation calls obtained from the HiSeq 2500 and HiSeq X Ten, as demonstrated using DNA from a cell line, clinical sample and FFPET sample (Pearson r > 0.94) (Fig. a).

    Techniques: Bisulfite Sequencing

    The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).

    Journal: PLoS ONE

    Article Title: Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing

    doi: 10.1371/journal.pone.0190264

    Figure Lengend Snippet: The sequence coverage of germline variants and the length of the indels which were identified in one sequence platform. Read depth in Illumina for variants unique to BGISEQ-500 ( a ) read depth in BGI for variants unique to Illumina ( b ). The distribution of the length (number of bases) of the indels that were identified in both sequencing platforms or unique to the HiSeq X Ten or BGISEQ-500 data is plotted ( c ).

    Article Snippet: In this study we performed whole genome sequencing of three malignant pleural mesothelioma and matched normal samples using a new platform, the BGISEQ-500, and compared the results obtained with Illumina HiSeq X Ten.

    Techniques: Sequencing