gaiix Illumina Inc Search Results


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  • 94
    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 13775 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc illumina gaii
    The Methylacidiphilum fumariolicum SolV genome sequence. A) Circos plot depicts the level of concordance between draft genome and the final assembly. Coloured links highlight misassemblies in the draft genome. B) Circos plot illustrates the overall genetic makeup of the Methylacidiphilum fumariolicum SolV. The outer ring marks the positions of tandem repeats across the genome. The next rings (outside to inside) show: gene annotation, highlighting key biological pathways in colours; placement of the draft genome in respect to the final assembly; and the overall GC content and the coverage profile of SMRT, Roche 454, and <t>Illumina</t> <t>GAII</t> sequencing reads. Repetitive sequences and structural variations are linked across the genome. Repeats that are longer than 2 Kb are shown in red whilst shorter repeats are linked in grey.
    Illumina Gaii, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 4134 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc illumina gaiix platform
    DG template preparation workflow. Genomic DNA is digested with Fse I. Index adapters are ligated to the Fse I ends. The DNA fragments are randomly sheared, followed by size selection on agarose gels. DNA fragments of a selected size are end-repaired. A T-tailed adapter is ligated to the repaired ends of the DNA. PCR is carried out with a biotinylated oligonucleotide primer complementary to the Index adapter. DNA fragments labelled with biotin are captured via magnetic beads. The purified DNA fragments are amplified by PCR with <t>Illumina</t> Primers. Amplification products are sequenced on the Illumina <t>GAIIx</t> sequencer. The colored regions in the DNA fragments correspond to the colored regions in the detailed views of the Index and T-tailed adapters in Figure 6 .
    Illumina Gaiix Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 3501 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc illumina gaii platform
    <t>Illumina</t> <t>GAII</t> sequencing
    Illumina Gaii Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 1677 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    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 1664 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc cdna libraries
    Identification of sRNAs associated with the susC homologs of B. fragilis PULs by RNA-seq. (A) Representative <t>Illumina</t> reads of <t>cDNA</t> from the TEX (terminator exonuclease)-treated libraries enriched for primary transcripts. Each locus is designated by the
    Cdna Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 30682 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Illumina Inc illumina gaii sequencer
    Identification of sRNAs associated with the susC homologs of B. fragilis PULs by RNA-seq. (A) Representative <t>Illumina</t> reads of <t>cDNA</t> from the TEX (terminator exonuclease)-treated libraries enriched for primary transcripts. Each locus is designated by the
    Illumina Gaii Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 837 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc illumina hiseq 2000
    Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children. Analysis of 176 plasma and NP samples on the <t>Illumina</t> GAIIX and <t>HiSeq</t> 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.
    Illumina Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 49312 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc genome analyzer gaiix
    Schematic diagram of the workflow for O. melastigma miRNA discovery. Brain, liver and gonadal (ovary and testis) tissues of male and female marine medaka were submitted to small RNA libraries preparation and were sequenced using <t>Illumina</t> <t>GAIIX.</t> After the removal of low quality reads and filtering, high quality sequencing reads were blasted against miRBase v.17 to identify the conserved miRNAs of marine medaka.
    Genome Analyzer Gaiix, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 694 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc rna seq libraries
    Transcriptional start site of the PI-2b operon. (A) Characterization of PI-2b transcription start site in S . agalactiae strains A909 and BM110 by <t>dRNA-seq.</t> The sequence reads corresponding to transcript 5' ends generated after (TAP+) or without (TAP-) TAP treatment or obtained from strand-specific <t>RNA-seq</t> (RNA-seq) were aligned to the genomes of strains A909 and BM110. A significantly higher number of reads under TAP+ conditions as compared with TAP- is indicative of 5' -triphosphate ends of transcripts characteristic of transcription start sites (TSS). Identical TSS upstream PI-2b locus are detected in strains A909 and BM110. In addition, coverage of the intergenic regions between sak1445 (or san1522) and orf under conditions of RNA-seq experiments reveals a transcriptional read-through originating from sak1445 , in A909 only, that could participate to the global level of PI-2b transcription in A909. (B) Primer extension analysis of the PI-2b mRNA. Primer elongation product obtained with oligonucleotide E3 and 15 μg of total RNA from A909 (lane1) or BM110 (lane 2). Lanes T, G, C, A, results of sequencing reactions performed with primer E3. Arrow indicated the transcriptional start site. (C) Schematic representation and genomic DNA sequence, from nucleotide positions -281 to +3 (numbering from the A of the ATG start codon of orf , negative in the -3'-to-5' direction and positive in the 5' to-3' direction) of the region upstream from the PI-2b locus. Transcription start site is indicated in boldface and arrow. Consensus -10 and -35 sequences are indicated by grey boxes. The 43-bp sequence, present in BM110 and absent in A909, is underlined. The ATG start codon of orf is indicated in boldface.
    Rna Seq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 14521 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc genomic dna
    Approach used to identify SCNGs in this study. (A) Genes that were identified as putative SCNGs across different algorithmic studies were cross-referenced with public ESTs. (B) Loci for primer design were selected according to criteria outlined in the text. (C) Primer design was based on alignments of reads from shallow-depth <t>Illumina</t> sequencing of genomic <t>DNA</t> of Brassica rapa and B. oleracea (2× and 9× coverage, respectively) mapped onto the Arabidopsis thaliana genome. (D) Primers were tested in silico and in the laboratory before final selection for sequencing of products (E).
    Genomic Dna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 12613 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc illumina genome analyzer
    Consensus sequence quality. The proportion of 454 read data within the total read collection affected the number of small insertions and deletions (indels) based on analysis of 7,169 unique EST-to-genome alignments. The relative proportions of insertions (blue) and deletions (orange) in the assembly sequence are shown in the inset pie chart. Assemblies are described in Tables 1 and 2; those including 454 read data were assembled with Forge; the <t>Illumina-only</t> assembly was generated with Velvet.
    Illumina Genome Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 10837 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc gaii sequencing data
    Consensus sequence quality. The proportion of 454 read data within the total read collection affected the number of small insertions and deletions (indels) based on analysis of 7,169 unique EST-to-genome alignments. The relative proportions of insertions (blue) and deletions (orange) in the assembly sequence are shown in the inset pie chart. Assemblies are described in Tables 1 and 2; those including 454 read data were assembled with Forge; the <t>Illumina-only</t> assembly was generated with Velvet.
    Gaii Sequencing Data, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 193 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 90 stars, based on 193 article reviews
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    92
    Illumina Inc illumina gaiix sequencing
    Consensus sequence quality. The proportion of 454 read data within the total read collection affected the number of small insertions and deletions (indels) based on analysis of 7,169 unique EST-to-genome alignments. The relative proportions of insertions (blue) and deletions (orange) in the assembly sequence are shown in the inset pie chart. Assemblies are described in Tables 1 and 2; those including 454 read data were assembled with Forge; the <t>Illumina-only</t> assembly was generated with Velvet.
    Illumina Gaiix Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 92/100, based on 569 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc gaiix sequencing platform
    SNP discovery pipeline using <t>Illumina</t> <t>GAIIx</t> sequence reads of eight flax genotypes aligned against the whole genome shotgun sequence assembly of CDC Bethune.
    Gaiix Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 255 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    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.

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

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

    doi: 10.1073/pnas.1319397111

    Figure Lengend 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.

    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.

    Techniques: Labeling, Isolation, Expressing

    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 Methylacidiphilum fumariolicum SolV genome sequence. A) Circos plot depicts the level of concordance between draft genome and the final assembly. Coloured links highlight misassemblies in the draft genome. B) Circos plot illustrates the overall genetic makeup of the Methylacidiphilum fumariolicum SolV. The outer ring marks the positions of tandem repeats across the genome. The next rings (outside to inside) show: gene annotation, highlighting key biological pathways in colours; placement of the draft genome in respect to the final assembly; and the overall GC content and the coverage profile of SMRT, Roche 454, and Illumina GAII sequencing reads. Repetitive sequences and structural variations are linked across the genome. Repeats that are longer than 2 Kb are shown in red whilst shorter repeats are linked in grey.

    Journal: BMC Genomics

    Article Title: The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV

    doi: 10.1186/1471-2164-15-914

    Figure Lengend Snippet: The Methylacidiphilum fumariolicum SolV genome sequence. A) Circos plot depicts the level of concordance between draft genome and the final assembly. Coloured links highlight misassemblies in the draft genome. B) Circos plot illustrates the overall genetic makeup of the Methylacidiphilum fumariolicum SolV. The outer ring marks the positions of tandem repeats across the genome. The next rings (outside to inside) show: gene annotation, highlighting key biological pathways in colours; placement of the draft genome in respect to the final assembly; and the overall GC content and the coverage profile of SMRT, Roche 454, and Illumina GAII sequencing reads. Repetitive sequences and structural variations are linked across the genome. Repeats that are longer than 2 Kb are shown in red whilst shorter repeats are linked in grey.

    Article Snippet: Moreover, 99.9% of Illumina GAII and Roche 454 reads (Additional file : Table S1, Figures S4 and S5) that were used to assemble the draft genome [ ] mapped to the complete genome sequence (Figure B).

    Techniques: Sequencing

    DG template preparation workflow. Genomic DNA is digested with Fse I. Index adapters are ligated to the Fse I ends. The DNA fragments are randomly sheared, followed by size selection on agarose gels. DNA fragments of a selected size are end-repaired. A T-tailed adapter is ligated to the repaired ends of the DNA. PCR is carried out with a biotinylated oligonucleotide primer complementary to the Index adapter. DNA fragments labelled with biotin are captured via magnetic beads. The purified DNA fragments are amplified by PCR with Illumina Primers. Amplification products are sequenced on the Illumina GAIIx sequencer. The colored regions in the DNA fragments correspond to the colored regions in the detailed views of the Index and T-tailed adapters in Figure 6 .

    Journal: BMC Genomics

    Article Title: Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome

    doi: 10.1186/1471-2164-14-448

    Figure Lengend Snippet: DG template preparation workflow. Genomic DNA is digested with Fse I. Index adapters are ligated to the Fse I ends. The DNA fragments are randomly sheared, followed by size selection on agarose gels. DNA fragments of a selected size are end-repaired. A T-tailed adapter is ligated to the repaired ends of the DNA. PCR is carried out with a biotinylated oligonucleotide primer complementary to the Index adapter. DNA fragments labelled with biotin are captured via magnetic beads. The purified DNA fragments are amplified by PCR with Illumina Primers. Amplification products are sequenced on the Illumina GAIIx sequencer. The colored regions in the DNA fragments correspond to the colored regions in the detailed views of the Index and T-tailed adapters in Figure 6 .

    Article Snippet: After sequencing on the Illumina GAIIx platform, the raw sequencing reads are processed and deconvoluted into individual groups by barcode.

    Techniques: Selection, Polymerase Chain Reaction, Magnetic Beads, Purification, Amplification

    Pooling scheme for sequencing experiment 2. We selected 96 samples across three 384-well plates based on their position on the plate, such that each sample was present in exactly 3 of the 72 pools and majority of the samples can be uniquely identified based on the pattern of positive pools. For the first 24 pools, samples in the same columns were combined. For the next 24 pools, samples in the same rows were combined. Lastly, samples in the same well position across plates were combined into a total of 24 pools. This pooling scheme resulted in a total of 72 pools that can be sequenced in six lanes on Illumina Genome Analyzer IIx platform.

    Journal: Nucleic Acids Research

    Article Title: Efficient identification of rare variants in large populations: deep re-sequencing the CRP locus in the CARDIA study

    doi: 10.1093/nar/gkt092

    Figure Lengend Snippet: Pooling scheme for sequencing experiment 2. We selected 96 samples across three 384-well plates based on their position on the plate, such that each sample was present in exactly 3 of the 72 pools and majority of the samples can be uniquely identified based on the pattern of positive pools. For the first 24 pools, samples in the same columns were combined. For the next 24 pools, samples in the same rows were combined. Lastly, samples in the same well position across plates were combined into a total of 24 pools. This pooling scheme resulted in a total of 72 pools that can be sequenced in six lanes on Illumina Genome Analyzer IIx platform.

    Article Snippet: This pooling scheme resulted in 24 pools overall, which were sequenced using two lanes on the Illumina Genome Analyzer IIx platform.

    Techniques: Sequencing

    Illumina GAII sequencing

    Journal: Genes, brain, and behavior

    Article Title: Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice

    doi: 10.1111/gbb.12018

    Figure Lengend Snippet: Illumina GAII sequencing

    Article Snippet: Quantitative RNA Sequencing was completed on an Illumina GAII platform.

    Techniques: Sequencing

    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

    Identification of sRNAs associated with the susC homologs of B. fragilis PULs by RNA-seq. (A) Representative Illumina reads of cDNA from the TEX (terminator exonuclease)-treated libraries enriched for primary transcripts. Each locus is designated by the

    Journal: Journal of Bacteriology

    Article Title: cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides

    doi: 10.1128/JB.00381-16

    Figure Lengend Snippet: Identification of sRNAs associated with the susC homologs of B. fragilis PULs by RNA-seq. (A) Representative Illumina reads of cDNA from the TEX (terminator exonuclease)-treated libraries enriched for primary transcripts. Each locus is designated by the

    Article Snippet: The cDNA libraries were sequenced using an Illumina GA IIx genome analyzer with 100 cycles.

    Techniques: RNA Sequencing Assay

    Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children. Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.

    Journal: PLoS ONE

    Article Title: Sequence Analysis of the Human Virome in Febrile and Afebrile Children

    doi: 10.1371/journal.pone.0027735

    Figure Lengend Snippet: Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children. Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.

    Article Snippet: For samples in which additional sequencing reads were generated, the Illumina GAIIX or Illumina HiSeq 2000 was used ( ).

    Techniques: Sequencing

    Comparison of error rates for each type of nucleotide change for spike-in standard or genome recalibration with (a) SOLiD 4 data with standards spiked-in in a large dynamic concentration range or (b) Illumina HiSeq data with standards spiked-in at equimolar concentrations. The plots are annotated with transition/transversion (Ti/Tv) ratios, where random base changes result in Ti/Tv = 0.5, and biological mutations result in Ti/Tv > > 0.5. To determine the significance of biological variants in the data, only bases with reported reported base quality scores above 30 are included in this analysis. All values are the mean ± SD of 2 samples with 2 biological replicates or of 4 sequenced samples with no replicates.

    Journal: PLoS ONE

    Article Title: Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

    doi: 10.1371/journal.pone.0041356

    Figure Lengend Snippet: Comparison of error rates for each type of nucleotide change for spike-in standard or genome recalibration with (a) SOLiD 4 data with standards spiked-in in a large dynamic concentration range or (b) Illumina HiSeq data with standards spiked-in at equimolar concentrations. The plots are annotated with transition/transversion (Ti/Tv) ratios, where random base changes result in Ti/Tv = 0.5, and biological mutations result in Ti/Tv > > 0.5. To determine the significance of biological variants in the data, only bases with reported reported base quality scores above 30 are included in this analysis. All values are the mean ± SD of 2 samples with 2 biological replicates or of 4 sequenced samples with no replicates.

    Article Snippet: Similar to our results in which the CG error rate is high both for Illumina and SOLiD when recalibrating based on the genome, their results also show high CG error rates for DNA sequencing for all platforms, including Illumina GaIIx, Illumina HiSeq, SOLiD, and 454.

    Techniques: Concentration Assay

    BQSR recalibration inaccuracies due to limited size and coverage of the ERCC spike-in standards, compared to the inaccuracies caused by recalibrating from the genome excluding known variant sites in dbSNP. The errors due to the limitations of the spike-in standards are the mean absolute difference between the recalibration coefficients calculated from randomly selected 50% of the spike-in standard bases (ERCC Set A) and the opposite 50% of the bases (ERCC Set B). Because the mean absolute differences are lower for the spike-in standards, they serve as a reasonable proxy for accuracy of the recalibration coefficients. Differences are calculated for the base quality score reported from the instrument (RpQS), dinucleotide context (Dinuc), and machine cycle (Cycle). The differences are the mean ± SD (n = 4) for SOLiD4 with spike-in standards spiked-in in a large dynamic concentration range with 250–700× mean coverage (SOLiD-DR), and for Illumina HiSeq with spike-in standards spiked-in at equimolar concentrations with 5500–8500× mean coverage (Illumina-EP). The use of spike-in standards for recalibration significantly improves upon the traditional genome recalibration in all cases (p

    Journal: PLoS ONE

    Article Title: Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

    doi: 10.1371/journal.pone.0041356

    Figure Lengend Snippet: BQSR recalibration inaccuracies due to limited size and coverage of the ERCC spike-in standards, compared to the inaccuracies caused by recalibrating from the genome excluding known variant sites in dbSNP. The errors due to the limitations of the spike-in standards are the mean absolute difference between the recalibration coefficients calculated from randomly selected 50% of the spike-in standard bases (ERCC Set A) and the opposite 50% of the bases (ERCC Set B). Because the mean absolute differences are lower for the spike-in standards, they serve as a reasonable proxy for accuracy of the recalibration coefficients. Differences are calculated for the base quality score reported from the instrument (RpQS), dinucleotide context (Dinuc), and machine cycle (Cycle). The differences are the mean ± SD (n = 4) for SOLiD4 with spike-in standards spiked-in in a large dynamic concentration range with 250–700× mean coverage (SOLiD-DR), and for Illumina HiSeq with spike-in standards spiked-in at equimolar concentrations with 5500–8500× mean coverage (Illumina-EP). The use of spike-in standards for recalibration significantly improves upon the traditional genome recalibration in all cases (p

    Article Snippet: Similar to our results in which the CG error rate is high both for Illumina and SOLiD when recalibrating based on the genome, their results also show high CG error rates for DNA sequencing for all platforms, including Illumina GaIIx, Illumina HiSeq, SOLiD, and 454.

    Techniques: Variant Assay, Concentration Assay

    Schematic diagram of the workflow for O. melastigma miRNA discovery. Brain, liver and gonadal (ovary and testis) tissues of male and female marine medaka were submitted to small RNA libraries preparation and were sequenced using Illumina GAIIX. After the removal of low quality reads and filtering, high quality sequencing reads were blasted against miRBase v.17 to identify the conserved miRNAs of marine medaka.

    Journal: PLoS ONE

    Article Title: Identification and Expression Profiling of MicroRNAs in the Brain, Liver and Gonads of Marine Medaka (Oryzias melastigma) and in Response to Hypoxia

    doi: 10.1371/journal.pone.0110698

    Figure Lengend Snippet: Schematic diagram of the workflow for O. melastigma miRNA discovery. Brain, liver and gonadal (ovary and testis) tissues of male and female marine medaka were submitted to small RNA libraries preparation and were sequenced using Illumina GAIIX. After the removal of low quality reads and filtering, high quality sequencing reads were blasted against miRBase v.17 to identify the conserved miRNAs of marine medaka.

    Article Snippet: Sequencing was performed on the Illumina Genome Analyzer GAIIx.

    Techniques: Sequencing

    A sex-specific timecourse of early-embryonic gene expression. (A) Transcription events during early embryogenesis. During the first 8–9 mitotic cycles, almost all RNAs in the embryo are of maternal origin. Zygotic transcription begins at a low level at approximately cycle 10 and becomes widespread by the middle of cycle 14. MSL-mediated dosage compensation begins late in or following cycle 14. (B) Embryos used for mRNA-Seq. Individual embryos in the interphases of cycles 10 to 14 were selected by direct observation of mitosis in embryos containing histone H2Av-RFP and computing nuclear density. Embryos at substages of cycle 14 were selected by observing the extent of progression through cellularization (from proportion of membrane invagination) under light microscopy. Each embryo pictured here was placed into TRIzol reagent immediately after these images were taken, DNA and RNA were extracted, and each sample was genotyped to determine the sex of the embryo. (C) Approximately 100 ng total RNA was obtained from each embryo, and poly-A RNA was processed with an amplification-free protocol optimized for small samples and sequenced on an Illumina GAIIx Genome Analyzer. Data (normalized reads per kb, RPKM) from independently processed individuals of the same stage and same sex, and same stage but different sex were extremely similar, while individuals from different stages showed larger numbers of differences.

    Journal: PLoS Biology

    Article Title: Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-SeqDoubling the Dose

    doi: 10.1371/journal.pbio.1000590

    Figure Lengend Snippet: A sex-specific timecourse of early-embryonic gene expression. (A) Transcription events during early embryogenesis. During the first 8–9 mitotic cycles, almost all RNAs in the embryo are of maternal origin. Zygotic transcription begins at a low level at approximately cycle 10 and becomes widespread by the middle of cycle 14. MSL-mediated dosage compensation begins late in or following cycle 14. (B) Embryos used for mRNA-Seq. Individual embryos in the interphases of cycles 10 to 14 were selected by direct observation of mitosis in embryos containing histone H2Av-RFP and computing nuclear density. Embryos at substages of cycle 14 were selected by observing the extent of progression through cellularization (from proportion of membrane invagination) under light microscopy. Each embryo pictured here was placed into TRIzol reagent immediately after these images were taken, DNA and RNA were extracted, and each sample was genotyped to determine the sex of the embryo. (C) Approximately 100 ng total RNA was obtained from each embryo, and poly-A RNA was processed with an amplification-free protocol optimized for small samples and sequenced on an Illumina GAIIx Genome Analyzer. Data (normalized reads per kb, RPKM) from independently processed individuals of the same stage and same sex, and same stage but different sex were extremely similar, while individuals from different stages showed larger numbers of differences.

    Article Snippet: We sequenced a total of 24 mRNA samples on an Illumina GAIIx Genome Analyzer.

    Techniques: Expressing, Light Microscopy, Amplification

    Transcriptional start site of the PI-2b operon. (A) Characterization of PI-2b transcription start site in S . agalactiae strains A909 and BM110 by dRNA-seq. The sequence reads corresponding to transcript 5' ends generated after (TAP+) or without (TAP-) TAP treatment or obtained from strand-specific RNA-seq (RNA-seq) were aligned to the genomes of strains A909 and BM110. A significantly higher number of reads under TAP+ conditions as compared with TAP- is indicative of 5' -triphosphate ends of transcripts characteristic of transcription start sites (TSS). Identical TSS upstream PI-2b locus are detected in strains A909 and BM110. In addition, coverage of the intergenic regions between sak1445 (or san1522) and orf under conditions of RNA-seq experiments reveals a transcriptional read-through originating from sak1445 , in A909 only, that could participate to the global level of PI-2b transcription in A909. (B) Primer extension analysis of the PI-2b mRNA. Primer elongation product obtained with oligonucleotide E3 and 15 μg of total RNA from A909 (lane1) or BM110 (lane 2). Lanes T, G, C, A, results of sequencing reactions performed with primer E3. Arrow indicated the transcriptional start site. (C) Schematic representation and genomic DNA sequence, from nucleotide positions -281 to +3 (numbering from the A of the ATG start codon of orf , negative in the -3'-to-5' direction and positive in the 5' to-3' direction) of the region upstream from the PI-2b locus. Transcription start site is indicated in boldface and arrow. Consensus -10 and -35 sequences are indicated by grey boxes. The 43-bp sequence, present in BM110 and absent in A909, is underlined. The ATG start codon of orf is indicated in boldface.

    Journal: PLoS ONE

    Article Title: Regulation of PI-2b Pilus Expression in Hypervirulent Streptococcus agalactiae ST-17 BM110

    doi: 10.1371/journal.pone.0169840

    Figure Lengend Snippet: Transcriptional start site of the PI-2b operon. (A) Characterization of PI-2b transcription start site in S . agalactiae strains A909 and BM110 by dRNA-seq. The sequence reads corresponding to transcript 5' ends generated after (TAP+) or without (TAP-) TAP treatment or obtained from strand-specific RNA-seq (RNA-seq) were aligned to the genomes of strains A909 and BM110. A significantly higher number of reads under TAP+ conditions as compared with TAP- is indicative of 5' -triphosphate ends of transcripts characteristic of transcription start sites (TSS). Identical TSS upstream PI-2b locus are detected in strains A909 and BM110. In addition, coverage of the intergenic regions between sak1445 (or san1522) and orf under conditions of RNA-seq experiments reveals a transcriptional read-through originating from sak1445 , in A909 only, that could participate to the global level of PI-2b transcription in A909. (B) Primer extension analysis of the PI-2b mRNA. Primer elongation product obtained with oligonucleotide E3 and 15 μg of total RNA from A909 (lane1) or BM110 (lane 2). Lanes T, G, C, A, results of sequencing reactions performed with primer E3. Arrow indicated the transcriptional start site. (C) Schematic representation and genomic DNA sequence, from nucleotide positions -281 to +3 (numbering from the A of the ATG start codon of orf , negative in the -3'-to-5' direction and positive in the 5' to-3' direction) of the region upstream from the PI-2b locus. Transcription start site is indicated in boldface and arrow. Consensus -10 and -35 sequences are indicated by grey boxes. The 43-bp sequence, present in BM110 and absent in A909, is underlined. The ATG start codon of orf is indicated in boldface.

    Article Snippet: In addition, strand-specific RNA-seq libraries were prepared from the two strains grown at mid-exponential growth phase by using the Illumina primer ligation method. dRNA-seq and RNA-seq libraries were sequenced on the Illumina GAIIX or HiSeq 2000.

    Techniques: Sequencing, Generated, RNA Sequencing Assay

    Approach used to identify SCNGs in this study. (A) Genes that were identified as putative SCNGs across different algorithmic studies were cross-referenced with public ESTs. (B) Loci for primer design were selected according to criteria outlined in the text. (C) Primer design was based on alignments of reads from shallow-depth Illumina sequencing of genomic DNA of Brassica rapa and B. oleracea (2× and 9× coverage, respectively) mapped onto the Arabidopsis thaliana genome. (D) Primers were tested in silico and in the laboratory before final selection for sequencing of products (E).

    Journal: Applications in Plant Sciences

    Article Title: Single-copy nuclear gene primers for Streptanthus and other Brassicaceae from genomic scans, published data, and ESTs 1

    doi: 10.3732/apps.1200002

    Figure Lengend Snippet: Approach used to identify SCNGs in this study. (A) Genes that were identified as putative SCNGs across different algorithmic studies were cross-referenced with public ESTs. (B) Loci for primer design were selected according to criteria outlined in the text. (C) Primer design was based on alignments of reads from shallow-depth Illumina sequencing of genomic DNA of Brassica rapa and B. oleracea (2× and 9× coverage, respectively) mapped onto the Arabidopsis thaliana genome. (D) Primers were tested in silico and in the laboratory before final selection for sequencing of products (E).

    Article Snippet: We designed primers based on alignments of genomic scans generated from low-coverage Illumina sequencing of total genomic DNA (Illumina GAIIx [Illumina Inc., San Diego, California, USA], 80 bp reads) of B. rapa L. (2× coverage) and B. oleracea L. (9× coverage; L. Comai, unpublished data) mapped onto A. thaliana using the Burrows-Wheeler Alignment tool (BWA) ( ) and visualized in IGV version 1.5 ( ).

    Techniques: Sequencing, In Silico, Selection

    Consensus sequence quality. The proportion of 454 read data within the total read collection affected the number of small insertions and deletions (indels) based on analysis of 7,169 unique EST-to-genome alignments. The relative proportions of insertions (blue) and deletions (orange) in the assembly sequence are shown in the inset pie chart. Assemblies are described in Tables 1 and 2; those including 454 read data were assembled with Forge; the Illumina-only assembly was generated with Velvet.

    Journal: Genome Biology

    Article Title: De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    doi: 10.1186/gb-2009-10-9-r94

    Figure Lengend Snippet: Consensus sequence quality. The proportion of 454 read data within the total read collection affected the number of small insertions and deletions (indels) based on analysis of 7,169 unique EST-to-genome alignments. The relative proportions of insertions (blue) and deletions (orange) in the assembly sequence are shown in the inset pie chart. Assemblies are described in Tables 1 and 2; those including 454 read data were assembled with Forge; the Illumina-only assembly was generated with Velvet.

    Article Snippet: To generate the draft sequence, we combined: conventional, 40-kb fosmid paired-end (PE) Sanger reads from an ABI 3730xl sequencer; single-end (SE) 454 reads from Roche GS20 and GS-FLX sequencers; and PE reads from an Illumina Genome Analyzer (GAii ) sequencer.

    Techniques: Sequencing, Generated

    Comparison of Forge Sanger/454/Illumina assemblies against GC gb1. Alignments of scaffolds greater that 100 kb - (a) 'Sanger/454/IlluminaDA' (approximately 24 Mb on 80 scaffolds) and (b) 'Sanger/454/IlluminaPA' (approximately 28.7 Mb on 46 scaffolds) - on the y-axis against the manually finished genome sequence ( GC gb1) on the x-axis.

    Journal: Genome Biology

    Article Title: De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    doi: 10.1186/gb-2009-10-9-r94

    Figure Lengend Snippet: Comparison of Forge Sanger/454/Illumina assemblies against GC gb1. Alignments of scaffolds greater that 100 kb - (a) 'Sanger/454/IlluminaDA' (approximately 24 Mb on 80 scaffolds) and (b) 'Sanger/454/IlluminaPA' (approximately 28.7 Mb on 46 scaffolds) - on the y-axis against the manually finished genome sequence ( GC gb1) on the x-axis.

    Article Snippet: To generate the draft sequence, we combined: conventional, 40-kb fosmid paired-end (PE) Sanger reads from an ABI 3730xl sequencer; single-end (SE) 454 reads from Roche GS20 and GS-FLX sequencers; and PE reads from an Illumina Genome Analyzer (GAii ) sequencer.

    Techniques: Sequencing

    Assessing the discovery of unique read information between the Illumina and 454 platforms. (a) Raw reads were processed into overlapping 28-bp k -mers, and any k -mer that varied from all other k -mers by at least 1 bp was accepted as new sequence information. The analysis was done separately for unique k -mers and those that occurred at least twice (2× k -mers). (b) MAQ was then used to map these k -mers to the reference genome sequence and the rate at which new coverage was generated was plotted against the number of k -mers examined.

    Journal: Genome Biology

    Article Title: De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

    doi: 10.1186/gb-2009-10-9-r94

    Figure Lengend Snippet: Assessing the discovery of unique read information between the Illumina and 454 platforms. (a) Raw reads were processed into overlapping 28-bp k -mers, and any k -mer that varied from all other k -mers by at least 1 bp was accepted as new sequence information. The analysis was done separately for unique k -mers and those that occurred at least twice (2× k -mers). (b) MAQ was then used to map these k -mers to the reference genome sequence and the rate at which new coverage was generated was plotted against the number of k -mers examined.

    Article Snippet: To generate the draft sequence, we combined: conventional, 40-kb fosmid paired-end (PE) Sanger reads from an ABI 3730xl sequencer; single-end (SE) 454 reads from Roche GS20 and GS-FLX sequencers; and PE reads from an Illumina Genome Analyzer (GAii ) sequencer.

    Techniques: Sequencing, Generated

    SNP discovery pipeline using Illumina GAIIx sequence reads of eight flax genotypes aligned against the whole genome shotgun sequence assembly of CDC Bethune.

    Journal: BMC Genomics

    Article Title: Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

    doi: 10.1186/1471-2164-13-684

    Figure Lengend Snippet: SNP discovery pipeline using Illumina GAIIx sequence reads of eight flax genotypes aligned against the whole genome shotgun sequence assembly of CDC Bethune.

    Article Snippet: Illumina sequencing RRL construction from the 350-425bp fraction and Illumina/Solexa sequencing [ ] was performed using Illumina GAIIx sequencing platform (Illumina Inc., San Diego, USA) by the Michael Smith Genome Sciences Centre of the BC Cancer Agency, Genome British Columbia (Vancouver, BC, Canada).

    Techniques: Sequencing

    Relationship of SNP discovery with sequence coverage and read depth in seven flax genotypes. ( A ) Read depth frequency distribution of 55,465 SNP locations identified by alignment of Illumina GAIIx reads of seven genotypes against the CDC Bethune whole genome shotgun sequence assembly. A minimum of three reads per genotype was required for SNP calling. A log scale was used for the number of SNPs because of the disproportion in the 3-50 reads bin. ( B ) Correlation of SNP discovery with sequence coverage expressed as genome equivalents (BT-CDC Bethune, MB-Macbeth, SP-SP2047, UG-UGG5-5, DL-Double Low, CT-Crepitam Tabor, G11-G-1186/94, AT-Atlas).

    Journal: BMC Genomics

    Article Title: Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries

    doi: 10.1186/1471-2164-13-684

    Figure Lengend Snippet: Relationship of SNP discovery with sequence coverage and read depth in seven flax genotypes. ( A ) Read depth frequency distribution of 55,465 SNP locations identified by alignment of Illumina GAIIx reads of seven genotypes against the CDC Bethune whole genome shotgun sequence assembly. A minimum of three reads per genotype was required for SNP calling. A log scale was used for the number of SNPs because of the disproportion in the 3-50 reads bin. ( B ) Correlation of SNP discovery with sequence coverage expressed as genome equivalents (BT-CDC Bethune, MB-Macbeth, SP-SP2047, UG-UGG5-5, DL-Double Low, CT-Crepitam Tabor, G11-G-1186/94, AT-Atlas).

    Article Snippet: Illumina sequencing RRL construction from the 350-425bp fraction and Illumina/Solexa sequencing [ ] was performed using Illumina GAIIx sequencing platform (Illumina Inc., San Diego, USA) by the Michael Smith Genome Sciences Centre of the BC Cancer Agency, Genome British Columbia (Vancouver, BC, Canada).

    Techniques: Sequencing