Structured Review

Illumina Inc genome analyzer iix
Defective homeostatic responses of F5 T cells in the absence of IKK2. F5 T cells from F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx (IKK2 ko) and huCD2 iCre- littermates (IKK2 wt) were labeled with CTV cell dye, mixed ∼1:1, and 2 × 10 6 total cells were transferred to either Rag1 −/− , Il15ra −/− Rag1 −/− , Il7 −/− Rag1 −/− or Ly5.1 F5 Rag1 −/− hosts for 14 d. ( A ) Histograms are of cell dye labeling in the indicated host by the indicted donor population at d7 and d14 after transfer. ( B ) Relative cell frequencies of YFP + and YFP − ). Graphs show ratio of YFP + :YFP − F5 T cells, normalized to input ratio at day 1 after transfer in the indicated hosts. ( C ) mRNA was isolated from sorted CD8 + TCR hi T cells from F5 Rag1 −/− Ikk2 fx /fx R26R EYFP huCD2 iCre and huCD2 iCre -ve littermate. Total mRNA was sequenced by a <t>Illumina</t> Genome Analyzer <t>IIx.</t> Following normalization reads were displayed as normalized reads per kilobase of exon per million reads (nRPKM). Bar charts show expression level (nRPKM) of the indicated genes in control F5 Rag1 −/− huCD2 iCre- R26R EYFP Ikk2 fx/fx samples (black bars; IKK2 WT) vs. F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx samples (red bars; IKK2 KO). Data are mean ± SD RPKM from triplicate biological replicates. ( D ) Graphs shows cell recovery from spleen, normalized to day 1, of IKK2 WT and IKK2 KO F5 T cells cotransferred to Il7 −/− Rag1 −/− hosts. Data are representative of five independent experiments.
Genome Analyzer Iix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 68 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/genome analyzer iix/product/Illumina Inc
Average 94 stars, based on 68 article reviews
Price from $9.99 to $1999.99
genome analyzer iix - by Bioz Stars, 2020-09
94/100 stars

Images

1) Product Images from "NF-?B signaling mediates homeostatic maturation of new T cells"

Article Title: NF-?B signaling mediates homeostatic maturation of new T cells

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1319397111

Defective homeostatic responses of F5 T cells in the absence of IKK2. F5 T cells from F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx (IKK2 ko) and huCD2 iCre- littermates (IKK2 wt) were labeled with CTV cell dye, mixed ∼1:1, and 2 × 10 6 total cells were transferred to either Rag1 −/− , Il15ra −/− Rag1 −/− , Il7 −/− Rag1 −/− or Ly5.1 F5 Rag1 −/− hosts for 14 d. ( A ) Histograms are of cell dye labeling in the indicated host by the indicted donor population at d7 and d14 after transfer. ( B ) Relative cell frequencies of YFP + and YFP − ). Graphs show ratio of YFP + :YFP − F5 T cells, normalized to input ratio at day 1 after transfer in the indicated hosts. ( C ) mRNA was isolated from sorted CD8 + TCR hi T cells from F5 Rag1 −/− Ikk2 fx /fx R26R EYFP huCD2 iCre and huCD2 iCre -ve littermate. Total mRNA was sequenced by a Illumina Genome Analyzer IIx. Following normalization reads were displayed as normalized reads per kilobase of exon per million reads (nRPKM). Bar charts show expression level (nRPKM) of the indicated genes in control F5 Rag1 −/− huCD2 iCre- R26R EYFP Ikk2 fx/fx samples (black bars; IKK2 WT) vs. F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx samples (red bars; IKK2 KO). Data are mean ± SD RPKM from triplicate biological replicates. ( D ) Graphs shows cell recovery from spleen, normalized to day 1, of IKK2 WT and IKK2 KO F5 T cells cotransferred to Il7 −/− Rag1 −/− hosts. Data are representative of five independent experiments.
Figure Legend Snippet: Defective homeostatic responses of F5 T cells in the absence of IKK2. F5 T cells from F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx (IKK2 ko) and huCD2 iCre- littermates (IKK2 wt) were labeled with CTV cell dye, mixed ∼1:1, and 2 × 10 6 total cells were transferred to either Rag1 −/− , Il15ra −/− Rag1 −/− , Il7 −/− Rag1 −/− or Ly5.1 F5 Rag1 −/− hosts for 14 d. ( A ) Histograms are of cell dye labeling in the indicated host by the indicted donor population at d7 and d14 after transfer. ( B ) Relative cell frequencies of YFP + and YFP − ). Graphs show ratio of YFP + :YFP − F5 T cells, normalized to input ratio at day 1 after transfer in the indicated hosts. ( C ) mRNA was isolated from sorted CD8 + TCR hi T cells from F5 Rag1 −/− Ikk2 fx /fx R26R EYFP huCD2 iCre and huCD2 iCre -ve littermate. Total mRNA was sequenced by a Illumina Genome Analyzer IIx. Following normalization reads were displayed as normalized reads per kilobase of exon per million reads (nRPKM). Bar charts show expression level (nRPKM) of the indicated genes in control F5 Rag1 −/− huCD2 iCre- R26R EYFP Ikk2 fx/fx samples (black bars; IKK2 WT) vs. F5 Rag1 −/− huCD2 iCre+ R26R EYFP Ikk2 fx/fx samples (red bars; IKK2 KO). Data are mean ± SD RPKM from triplicate biological replicates. ( D ) Graphs shows cell recovery from spleen, normalized to day 1, of IKK2 WT and IKK2 KO F5 T cells cotransferred to Il7 −/− Rag1 −/− hosts. Data are representative of five independent experiments.

Techniques Used: Labeling, Isolation, Expressing

2) Product Images from "Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells"

Article Title: Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells

Journal: Stem cells (Dayton, Ohio)

doi: 10.1002/stem.1195

Whole genome mRNA sequencing and ABCG2 mRNA expression. Analysis of ABCG2 mRNA expression by an Illumina Genome Analyzer IIx in two BG01 samples (sample 1 and sample 2). (A and B): Sample 1 was sequenced in duplicate for verifying the reproducibility of the assay. (C): mRNA sequencing of a different passage of BG01 cells for analysis of the stability of gene expression within the same line. Gene-specific and transcript-specific expression of ABCG2 are defined by the average fragments per kilobase per million reads (FPKM). The levels of transcripts are classified into three categories (as indicated) based on the cutoff values of the average FPKM.
Figure Legend Snippet: Whole genome mRNA sequencing and ABCG2 mRNA expression. Analysis of ABCG2 mRNA expression by an Illumina Genome Analyzer IIx in two BG01 samples (sample 1 and sample 2). (A and B): Sample 1 was sequenced in duplicate for verifying the reproducibility of the assay. (C): mRNA sequencing of a different passage of BG01 cells for analysis of the stability of gene expression within the same line. Gene-specific and transcript-specific expression of ABCG2 are defined by the average fragments per kilobase per million reads (FPKM). The levels of transcripts are classified into three categories (as indicated) based on the cutoff values of the average FPKM.

Techniques Used: Sequencing, Expressing

3) Product Images from "Whole-transcriptome RNAseq analysis from minute amount of total RNA"

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkr547

( A ) Comparison of average mapping statistics of transcriptomic content among three datasets using 50 bp reads from Genome Analyzer IIx (Illumina, Inc.): cDNA libraries made from single RNA samples of mouse testis tissue in which mRNA was enriched from total RNA either by (i) TruSeq™ poly-A selection or by (ii) RiboMinus™ rRNA depletion and (iii) cDNA library in which cDNA was synthesized directly from total RNA (DNase treated and left untreated) using the Ovation® RNA-Seq system. ( B ) Complexity of libraries (percent of unique start sites, unique pairs out of total mapped reads): cDNA libraries of TruSeq™ poly-A selection, RiboMinus™ rRNA depletion and Ovation® RNA-seq amplification system (different input amounts of total RNA). The sample prepared using the Ovation® RNA-Seq system provided slightly higher percentage of unique start sites.
Figure Legend Snippet: ( A ) Comparison of average mapping statistics of transcriptomic content among three datasets using 50 bp reads from Genome Analyzer IIx (Illumina, Inc.): cDNA libraries made from single RNA samples of mouse testis tissue in which mRNA was enriched from total RNA either by (i) TruSeq™ poly-A selection or by (ii) RiboMinus™ rRNA depletion and (iii) cDNA library in which cDNA was synthesized directly from total RNA (DNase treated and left untreated) using the Ovation® RNA-Seq system. ( B ) Complexity of libraries (percent of unique start sites, unique pairs out of total mapped reads): cDNA libraries of TruSeq™ poly-A selection, RiboMinus™ rRNA depletion and Ovation® RNA-seq amplification system (different input amounts of total RNA). The sample prepared using the Ovation® RNA-Seq system provided slightly higher percentage of unique start sites.

Techniques Used: Selection, cDNA Library Assay, Synthesized, RNA Sequencing Assay, Amplification

4) Product Images from "Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells"

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells

Journal: Stem cells (Dayton, Ohio)

doi: 10.1002/stem.1531

Ago HITS-CLIP analysis of stromal and endothelial cells. (A): Basic experimental scheme of Ago HITS-CLIP as adapted from Chi et al. UV cross-linked cells are lyzed and treated with RNase to reduce the length of mRNA fragments. Ago is immune-precipitated with monoclonal anti-Ago antibody 2A8, P32-labeled 3′ RNA linker ligated (on-bead), and resolved by SDS-PAGE electrophoresis. The protein-RNA-complex is transferred to nitrocellulose and visualized by autoradiography. In the representative autoradiograph shown, a major band is seen ~110 kD and a more diffuse band at ~130 kD. The RNA-protein complex in the 110–130 kD region is isolated and a 5′ RNA linker is ligated. The isolated RNA is reverse transcribed and PCR amplified with Illumina-compatible primers to generate a cDNA library (typical agarose gel shown). The cDNA libraries are then gel purified and sequenced on Illumina GA IIx and resultant bioinformatically analyzed. (B): Distribution of aligned reads from HS27A samples to different gene annotations. (C): Correlation of consensus peaks between HS5 and HS27A. Coefficient of determination ( R 2 determined by corrplot [R-package]). (D): Correlation of consensus peaks between HS5 and hMSC. (E): Correlation of consensus peaks between HS27A and hMSC. (F): Correlation of consensus peaks between TrHBMEC and HUVEC. (G): Overlap of genes enriched by consensus peaks between stromal cells (HS5, HS27A, and hMSC). (H): Overlap of genes enriched by consensus peaks between endothelial cells (TrHBMEC and HUVEC). Abbreviations: hMSC, human mesenchymal stromal cell; HUVEC, human umbilical vein endothelial cell; TrHBMEC, transformed human bone marrow endothelial cells; UV, ultraviolet.
Figure Legend Snippet: Ago HITS-CLIP analysis of stromal and endothelial cells. (A): Basic experimental scheme of Ago HITS-CLIP as adapted from Chi et al. UV cross-linked cells are lyzed and treated with RNase to reduce the length of mRNA fragments. Ago is immune-precipitated with monoclonal anti-Ago antibody 2A8, P32-labeled 3′ RNA linker ligated (on-bead), and resolved by SDS-PAGE electrophoresis. The protein-RNA-complex is transferred to nitrocellulose and visualized by autoradiography. In the representative autoradiograph shown, a major band is seen ~110 kD and a more diffuse band at ~130 kD. The RNA-protein complex in the 110–130 kD region is isolated and a 5′ RNA linker is ligated. The isolated RNA is reverse transcribed and PCR amplified with Illumina-compatible primers to generate a cDNA library (typical agarose gel shown). The cDNA libraries are then gel purified and sequenced on Illumina GA IIx and resultant bioinformatically analyzed. (B): Distribution of aligned reads from HS27A samples to different gene annotations. (C): Correlation of consensus peaks between HS5 and HS27A. Coefficient of determination ( R 2 determined by corrplot [R-package]). (D): Correlation of consensus peaks between HS5 and hMSC. (E): Correlation of consensus peaks between HS27A and hMSC. (F): Correlation of consensus peaks between TrHBMEC and HUVEC. (G): Overlap of genes enriched by consensus peaks between stromal cells (HS5, HS27A, and hMSC). (H): Overlap of genes enriched by consensus peaks between endothelial cells (TrHBMEC and HUVEC). Abbreviations: hMSC, human mesenchymal stromal cell; HUVEC, human umbilical vein endothelial cell; TrHBMEC, transformed human bone marrow endothelial cells; UV, ultraviolet.

Techniques Used: Cross-linking Immunoprecipitation, Labeling, SDS Page, Electrophoresis, Autoradiography, Isolation, Polymerase Chain Reaction, Amplification, cDNA Library Assay, Agarose Gel Electrophoresis, Purification, Transformation Assay

5) Product Images from "Astrovirus MLB2 Viremia in Febrile Child"

Article Title: Astrovirus MLB2 Viremia in Febrile Child

Journal: Emerging Infectious Diseases

doi: 10.3201/eid1711.110496

Map of 10 plasma-derived astrovirus MLB2 strain contigs generated by high-throughput sequencing (Genome Analyzer IIX; Illumina Inc., San Diego, CA, USA). ORF, open reading frame.
Figure Legend Snippet: Map of 10 plasma-derived astrovirus MLB2 strain contigs generated by high-throughput sequencing (Genome Analyzer IIX; Illumina Inc., San Diego, CA, USA). ORF, open reading frame.

Techniques Used: Derivative Assay, Generated, Next-Generation Sequencing

6) Product Images from "Whole-transcriptome RNAseq analysis from minute amount of total RNA"

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkr547

( A ) Comparison of average mapping statistics of transcriptomic content among three datasets using 50 bp reads from Genome Analyzer IIx (Illumina, Inc.): cDNA libraries made from single RNA samples of mouse testis tissue in which mRNA was enriched from total RNA either by (i) TruSeq™ poly-A selection or by (ii) RiboMinus™ rRNA depletion and (iii) cDNA library in which cDNA was synthesized directly from total RNA (DNase treated and left untreated) using the Ovation® RNA-Seq system. ( B ) Complexity of libraries (percent of unique start sites, unique pairs out of total mapped reads): cDNA libraries of TruSeq™ poly-A selection, RiboMinus™ rRNA depletion and Ovation® RNA-seq amplification system (different input amounts of total RNA). The sample prepared using the Ovation® RNA-Seq system provided slightly higher percentage of unique start sites.
Figure Legend Snippet: ( A ) Comparison of average mapping statistics of transcriptomic content among three datasets using 50 bp reads from Genome Analyzer IIx (Illumina, Inc.): cDNA libraries made from single RNA samples of mouse testis tissue in which mRNA was enriched from total RNA either by (i) TruSeq™ poly-A selection or by (ii) RiboMinus™ rRNA depletion and (iii) cDNA library in which cDNA was synthesized directly from total RNA (DNase treated and left untreated) using the Ovation® RNA-Seq system. ( B ) Complexity of libraries (percent of unique start sites, unique pairs out of total mapped reads): cDNA libraries of TruSeq™ poly-A selection, RiboMinus™ rRNA depletion and Ovation® RNA-seq amplification system (different input amounts of total RNA). The sample prepared using the Ovation® RNA-Seq system provided slightly higher percentage of unique start sites.

Techniques Used: Selection, cDNA Library Assay, Synthesized, RNA Sequencing Assay, Amplification

7) Product Images from "Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells"

Article Title: Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells

Journal: Stem cells (Dayton, Ohio)

doi: 10.1002/stem.1195

Whole genome mRNA sequencing and ABCG2 mRNA expression. Analysis of ABCG2 mRNA expression by an Illumina Genome Analyzer IIx in two BG01 samples (sample 1 and sample 2). (A and B): Sample 1 was sequenced in duplicate for verifying the reproducibility of the assay. (C): mRNA sequencing of a different passage of BG01 cells for analysis of the stability of gene expression within the same line. Gene-specific and transcript-specific expression of ABCG2 are defined by the average fragments per kilobase per million reads (FPKM). The levels of transcripts are classified into three categories (as indicated) based on the cutoff values of the average FPKM.
Figure Legend Snippet: Whole genome mRNA sequencing and ABCG2 mRNA expression. Analysis of ABCG2 mRNA expression by an Illumina Genome Analyzer IIx in two BG01 samples (sample 1 and sample 2). (A and B): Sample 1 was sequenced in duplicate for verifying the reproducibility of the assay. (C): mRNA sequencing of a different passage of BG01 cells for analysis of the stability of gene expression within the same line. Gene-specific and transcript-specific expression of ABCG2 are defined by the average fragments per kilobase per million reads (FPKM). The levels of transcripts are classified into three categories (as indicated) based on the cutoff values of the average FPKM.

Techniques Used: Sequencing, Expressing

Related Articles

Selection:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

RNA Sequencing Assay:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Further, our analysis of 92.5 million mapped short read sequences of 50 bases for cDNA libraries using the SOLiD platform and 38.5 million mapped paired end reads (2×50 bases) from same set of eight mouse samples using Illumina Genome Analyzer IIx revealed substantial enrichment of reads for mRNA and negligible rRNA reads when prepared with the Ovation® RNA-Seq System (1.92 and 2.09% for SOLiD and Illumina platforms, respectively) Supplementary Figures S1 A and B. .. Generally, using routine cDNA synthesis protocols in cases where there is no depletion of rRNA before cDNA synthesis, RNA-seq data maps to rRNA > 75% of the time for libraries from both prokaryotes and eukaryotes ( , ).

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Next-Generation Sequencing:

Article Title: NF-?B signaling mediates homeostatic maturation of new T cells
Article Snippet: .. Samples were sequenced at the MRC National Institute for Medical Research High Throughput Sequencing Facility by using an Illumina Genome Analyzer IIx, and 36 base-pair single-end reads were obtained using the Illumina pipeline. ..

Generated:

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

Expressing:

Article Title: Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells
Article Snippet: .. To further confirm the ABCG2 mRNA expression profile, we used an Illumina Genome Analyzer IIx to quantitatively verify gene-specific and transcript-specific expression of ABCG2 as defined by the average fragments per kilobase per million reads (FPKM) ( ). .. We mapped gene-specific transcripts to approximately 21, 510 individual genes in three sequencing experiments of the representative line BG01.

Sequencing:

Article Title: Regulation and Expression of the ATP-binding Cassette Transporter ABCG2 in Human Embryonic Stem Cells
Article Snippet: .. RNA preparations and 36-bp paired mRNA sequencing using an Illumina Genome Analyzer IIx were performed according to the manufacturer’s instructions (SAIC-Frederick, Inc., Frederick, MD). .. Amplified and finally sequenced reads were mapped to human transcript sequences (version hg19) using "TopHat" ( ).

Article Title: Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells
Article Snippet: .. Sequencing was performed on an Illumina Genome Analyzer IIx (single end 50 base pair reads). ..

Article Title: Whole-transcriptome RNAseq analysis from minute amount of total RNA
Article Snippet: .. Basic sequencing data for comparison of RNA-seq methods We generated a total of 245 million reads from single sample cDNA libraries using Genome Analyzer IIx (Illumina, Inc.) in which cDNA was prepared from mRNA enriched either by TruSeq™ poly-A selection (128.2 million reads) or by RiboMinus™ (99.6 million reads) as well as from total RNA using NuGEN-Ovation® RNA-Seq System (17.1 million reads). ..

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    Illumina Inc illumina gaiix sequencer
    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, <t>Illumina</t> <t>GAIIx,</t> and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.
    Illumina Gaiix Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 314 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaiix sequencer/product/Illumina Inc
    Average 94 stars, based on 314 article reviews
    Price from $9.99 to $1999.99
    illumina gaiix sequencer - by Bioz Stars, 2020-09
    94/100 stars
      Buy from Supplier

    95
    Illumina Inc illumina gaiix
    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, <t>Illumina</t> <t>GAIIx,</t> and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.
    Illumina Gaiix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 1611 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina gaiix/product/Illumina Inc
    Average 95 stars, based on 1611 article reviews
    Price from $9.99 to $1999.99
    illumina gaiix - by Bioz Stars, 2020-09
    95/100 stars
      Buy from Supplier

    Image Search Results


    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Journal: BMC Systems Biology

    Article Title: Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome

    doi: 10.1186/1752-0509-6-S3-S21

    Figure Lengend Snippet: The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Article Snippet: The preparing the PE library and sequencing on the Illumina GAIIx sequencer were performed according to the standard Illumina protocols (Illumina, San Diego, CA, USA).

    Techniques: Next-Generation Sequencing, Sequencing

    The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Journal: Open Biology

    Article Title: Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

    doi: 10.1098/rsob.120061

    Figure Lengend Snippet: The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Article Snippet: Each exome sample was then sequenced as paired-end reads in a full lane of an Illumina GAIIx sequencer or as a multiplexed, bar-coded sample in an Illumina HiSeq sequencer, and the resultant reads aligned to the C57BL/6 mouse reference genome using the BWA aligner [ ].

    Techniques: Sequencing, Generated, Variant Assay, Polymerase Chain Reaction

    The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Journal: BMC Systems Biology

    Article Title: Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome

    doi: 10.1186/1752-0509-6-S3-S21

    Figure Lengend Snippet: The performance of assembly as increasing coverage depths . The performance of assembled contigs (A), N50 size (B) and total bases (C) for the three NGS technologies at increasing depths in simulation. The red line, green line and blue line show the performance of Roche 454, Illumina GAIIx, and ABI SOLiD platform, respectively. Reads from each platform were simulated by random subsampling. Summary of performance of each platform, 25×, 240× and 300× sequencing data generating from 454, GAIIx and SOLiD platforms was sufficient for de novo assembly.

    Article Snippet: If cost allowed, the optimal outcome can be achieved with the combinations of 454 GS-FLX, Illumina GAIIx, and SOLiD4 sequencing data at abovementioned coverage depths.

    Techniques: Next-Generation Sequencing, Sequencing

    The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Journal: Open Biology

    Article Title: Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models

    doi: 10.1098/rsob.120061

    Figure Lengend Snippet: The influence of sequence quality scores and read depth on the identification of true-positive and false-positive SNVs. ( a ) False-positive calls with respect to read depth and quality score, shown for a single exome dataset generated from the G3 nimbus mouse (technical replicate 1 from figure 3 ). Variant calls on this dataset were compared with the PCR-validated true-positive and false-positive SNVs called in the technical replicate exome datasets of the G3 nimbus proband. Green and red points are true- and false-positive SNV calls, respectively. The distribution of read depth frequencies over all exonic bases is indicated by the red line in the top graph. The red bars in the right-hand graph indicate the distribution of quality scores also ascertained for all exonic bases. ( b ) Results of simulation experiment performed to generate random subsets of a single exome dataset, being one of the triplicate exome runs for the nimbus proband (technical replicate 1). The panel shows tallies of true-positive heterozygous (green), false-positive heterozygous (red), true-positive homozygous (blue) and false-positive homozygous (grey) SNV calls plotted against the number of input reads, which are incremental proportions of an Illumina GAIIx lane. Numbers alongside the green dots indicate the median read depth determined for each true-positive data point. Plotted above are the proportions of the exome covered at 20× depth or better for each proportion of the input read set.

    Article Snippet: Each library sequenced on an Illumina GAIIx was sequenced on a single lane of an eight-lane flow-cell, whereas libraries sequenced on the Illumina HiSeq were multiplexed in a pool of 10 samples and sequenced together, and disambiguated using sample bar-coding.

    Techniques: Sequencing, Generated, Variant Assay, Polymerase Chain Reaction