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Illumina Inc hiseq 2000 sequencing runs
Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina <t>HiSeq</t> 2000 (Pearson r (98) = 0.93, p
Hiseq 2000 Sequencing Runs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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hiseq 2000 sequencing runs - by Bioz Stars, 2020-12
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Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

Journal: Nucleic Acids Research

doi: 10.1093/nar/gku607

Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p
Figure Legend Snippet: Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

Techniques Used: Sequencing

Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p
Figure Legend Snippet: Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

Techniques Used: Sequencing, Derivative Assay

Related Articles

Sequencing:

Article Title: Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “ Candidatus Endobugula sertula”
Article Snippet: .. Stranded RNA sequencing (RNA-seq) Illumina libraries were prepared with ∼300-bp inserts and subjected to two Illumina HiSeq 2000 sequencing runs, one at 2 × 101 bp and one at 2 × 151 bp. .. Sequence yields are shown in Table S1 in the supplemental material.

Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence
Article Snippet: .. The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR. .. Statistical analyses Comparisons between observed and expected proportions of errors at barcode positions and each of the possible types of substitution errors were made using χ2 tests (GraphPad Prism Version 5).

Polymerase Chain Reaction:

Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence
Article Snippet: .. The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR. .. Statistical analyses Comparisons between observed and expected proportions of errors at barcode positions and each of the possible types of substitution errors were made using χ2 tests (GraphPad Prism Version 5).

RNA Sequencing Assay:

Article Title: Lack of Overt Genome Reduction in the Bryostatin-Producing Bryozoan Symbiont “ Candidatus Endobugula sertula”
Article Snippet: .. Stranded RNA sequencing (RNA-seq) Illumina libraries were prepared with ∼300-bp inserts and subjected to two Illumina HiSeq 2000 sequencing runs, one at 2 × 101 bp and one at 2 × 151 bp. .. Sequence yields are shown in Table S1 in the supplemental material.

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    Illumina Inc hiseq 2000 sequencing runs
    Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina <t>HiSeq</t> 2000 (Pearson r (98) = 0.93, p
    Hiseq 2000 Sequencing Runs, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 7640 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 sequencing runs/product/Illumina Inc
    Average 86 stars, based on 7640 article reviews
    Price from $9.99 to $1999.99
    hiseq 2000 sequencing runs - by Bioz Stars, 2020-12
    86/100 stars
      Buy from Supplier

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    Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

    Journal: Nucleic Acids Research

    Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

    doi: 10.1093/nar/gku607

    Figure Lengend Snippet: Analysis of the relative abundance, GC content and likelihood of secondary structure formation for each of the 100 expected Illumina-compatible barcode sequences. ( A ) Relative abundance of the 100 expected barcode sequences, as detected during the first and second sequencing runs using the Illumina HiSeq 2000 (Pearson r (98) = 0.93, p

    Article Snippet: The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR.

    Techniques: Sequencing

    Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

    Journal: Nucleic Acids Research

    Article Title: Impact of next-generation sequencing error on analysis of barcoded plasmid libraries of known complexity and sequence

    doi: 10.1093/nar/gku607

    Figure Lengend Snippet: Analysis of the position and substitution-like type of error for all one-mismatch sequence errors for both Illumina HiSeq 2000 sequencing runs. One-mismatch errors were compared to the known barcode sequences from which they were derived. Errors from the first sequencing run represent the sum of one-mismatch errors after Q30 quality filtering for the one-barcode sample and 10- and 100-barcode libraries, although one-mismatch errors from the 100-barcode library comprise 95.3% of all errors. Errors from the second sequencing run represent one-mismatch errors after Q30 quality filtering for the 100-barcode library. ( A ) Distribution of one-mismatch errors across each position of the barcode (positions 2–16 of the sequence reads). This distribution differed significantly from an expected even distribution (χ 2 = 30 064, df = 14, p

    Article Snippet: The samples analyzed included the two post-amplification samples that were used in the Illumina HiSeq 2000 sequencing runs, of which insufficient quantities remained for analysis using semi-quantitative PCR.

    Techniques: Sequencing, Derivative Assay

    Electropherograms of DNA extracted from older museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the HiSeq 2000.

    Journal: PLoS ONE

    Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

    doi: 10.1371/journal.pone.0143929

    Figure Lengend Snippet: Electropherograms of DNA extracted from older museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the HiSeq 2000.

    Article Snippet: All 10 of these discarded sequences were from samples run on one Illumina HiSeq 2000 lane, a lane with a higher-than-ideal cluster density of 932k/mm2 .

    Techniques:

    Electropherograms of DNA extracted from younger museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the Illumina HiSeq 2000. Regions are not shown for  Bembidion musae  or  Bembidion  “Inuvik” 3984 as the DNA in those samples was sonicated prior to library preparation. For each specimen, age and total DNA in the extraction is also shown.

    Journal: PLoS ONE

    Article Title: Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

    doi: 10.1371/journal.pone.0143929

    Figure Lengend Snippet: Electropherograms of DNA extracted from younger museum specimens that were subsequently used in library preparation. Pale spikes at 35 and 10380 bases represent standards included in each analysis. Dark shaded regions, when present, correspond to range of fragments that were selected and sequenced on the Illumina HiSeq 2000. Regions are not shown for Bembidion musae or Bembidion “Inuvik” 3984 as the DNA in those samples was sonicated prior to library preparation. For each specimen, age and total DNA in the extraction is also shown.

    Article Snippet: All 10 of these discarded sequences were from samples run on one Illumina HiSeq 2000 lane, a lane with a higher-than-ideal cluster density of 932k/mm2 .

    Techniques: Sonication

    SEQC study design. This figure was modified from b presented in the related research manuscript 13 . Similar to the MAQC-I benchmarks, well characterized RNA samples A and B were augmented by samples C and D comprised of A and B in known mixing ratios 3:1 and 1:3, respectively. These allow tests for titration consistency and the correct recovery of the known mixing ratios. Synthetic RNAs from the External RNA Control Consortium (ERCC) were both pre-added to samples A and B before mixing and also sequenced separately to assess dynamic range (samples E and F). Samples were distributed to independent sites for RNA-Seq library construction and profiling by Illumina’s HiSeq 2000 (3+4x) and Life Technologies’ SOLiD 5500 (3+1x). In addition to the replicate libraries A1…D4 at each site, for each platform, one vendor-prepared library A5…D5 was being sequenced at all three official sites, giving a total of 24 libraries. At each site, each library has a unique barcode sequence and all libraries were pooled before sequencing, so each lane was sequencing the same material, allowing a study of lane specific effects. Samples A and B were also sequenced by Roche 454 GS FLX at different sites with two runs each but no library replicates.

    Journal: Scientific Data

    Article Title: Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq

    doi: 10.1038/sdata.2014.20

    Figure Lengend Snippet: SEQC study design. This figure was modified from b presented in the related research manuscript 13 . Similar to the MAQC-I benchmarks, well characterized RNA samples A and B were augmented by samples C and D comprised of A and B in known mixing ratios 3:1 and 1:3, respectively. These allow tests for titration consistency and the correct recovery of the known mixing ratios. Synthetic RNAs from the External RNA Control Consortium (ERCC) were both pre-added to samples A and B before mixing and also sequenced separately to assess dynamic range (samples E and F). Samples were distributed to independent sites for RNA-Seq library construction and profiling by Illumina’s HiSeq 2000 (3+4x) and Life Technologies’ SOLiD 5500 (3+1x). In addition to the replicate libraries A1…D4 at each site, for each platform, one vendor-prepared library A5…D5 was being sequenced at all three official sites, giving a total of 24 libraries. At each site, each library has a unique barcode sequence and all libraries were pooled before sequencing, so each lane was sequencing the same material, allowing a study of lane specific effects. Samples A and B were also sequenced by Roche 454 GS FLX at different sites with two runs each but no library replicates.

    Article Snippet: Equal amounts of pooled libraries were then loaded to each lane of 2 flow cells and run on HiSeq 2000 Sequencing Systems (Illumina) for paired-end 200 cycles.

    Techniques: Modification, Titration, RNA Sequencing Assay, Sequencing