Structured Review

Illumina Inc hiseq 2000
Frequency distribution of the contig sizes from two  Gynostemma  species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as assembled using Trinity.
Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 122 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/result/hiseq 2000/product/Illumina Inc
Average 94 stars, based on 122 article reviews
Price from $9.99 to $1999.99
hiseq 2000 - by Bioz Stars, 2020-07
94/100 stars

Images

1) Product Images from "Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)"

Article Title: Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)

Journal: Molecules

doi: 10.3390/molecules201219758

Frequency distribution of the contig sizes from two  Gynostemma  species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as assembled using Trinity.
Figure Legend Snippet: Frequency distribution of the contig sizes from two Gynostemma species. The frequency distribution of contig sizes resulting from Illumina HiSeq™ 2000 sequencing, as assembled using Trinity.

Techniques Used: Sequencing

2) Product Images from "Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling"

Article Title: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

Journal: Genome Biology

doi: 10.1186/gb-2012-13-10-r92

Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
Figure Legend Snippet: Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).

Techniques Used: In Silico, Produced, Sequencing

Related Articles

RNA Sequencing Assay:

Article Title: An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
Article Snippet: .. For 10 ccRCC samples, whole-genome sequencing and RNA sequencing were performed using HiSeq 2000, according to standard protocols recommended by Illumina. .. The mean sequencing depth for each sample was 65.9–223.0 ( Supplementary Table S1 and S2 ).

Construct:

Article Title: Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)
Article Snippet: .. Purified RNA was used to construct a directional cDNA library using the cDNA Synthesis Kit (Illumina), and then the cDNA library was sequenced using a HiSeq 2000 (Illumina) to obtain short sequences. ..

Article Title: Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)
Article Snippet: .. Paired‐end DNA sequencing libraries with ~500 bp of short inserts were constructed and sequenced on HiSeq™ 2000 or HiSeq™ 4000 platforms (Illumina, San Diego, CA). .. Raw sequencing reads with fewer than 5% missing (N ) bases and fewer than 50% of bases with a quality score < 5 were retained and used for alignment and SNP detection in later steps (Wu et al ., ).

Purification:

Article Title: Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)
Article Snippet: .. Purified RNA was used to construct a directional cDNA library using the cDNA Synthesis Kit (Illumina), and then the cDNA library was sequenced using a HiSeq 2000 (Illumina) to obtain short sequences. ..

cDNA Library Assay:

Article Title: Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae)
Article Snippet: .. Purified RNA was used to construct a directional cDNA library using the cDNA Synthesis Kit (Illumina), and then the cDNA library was sequenced using a HiSeq 2000 (Illumina) to obtain short sequences. ..

other:

Article Title: DNA copy number evolution in Drosophila cell lines
Article Snippet: The other cell lines used in this study, as well as an independent set of Cl.8 , were sequenced to have either 76 or 100 bp paired-end reads on a GAII or HiSeq 2000 (1182-4H , Cl.8+ , D16-c3 , D17-c3 , D20-c2 , D20-c5 , D4-c1 , D8 , D9 , L1 , mbn2 , S1 , S2R+ , S3 , Sg4 , and W2 ).

Article Title: The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)
Article Snippet: The library was sequenced on a HiSeq 2000.

DNA Sequencing:

Article Title: Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus)
Article Snippet: .. Paired‐end DNA sequencing libraries with ~500 bp of short inserts were constructed and sequenced on HiSeq™ 2000 or HiSeq™ 4000 platforms (Illumina, San Diego, CA). .. Raw sequencing reads with fewer than 5% missing (N ) bases and fewer than 50% of bases with a quality score < 5 were retained and used for alignment and SNP detection in later steps (Wu et al ., ).

Expressing:

Article Title: Transcriptome Analysis of Blunt Snout Bream (Megalobrama amblycephala) Reveals Putative Differential Expression Genes Related to Growth and Hypoxia
Article Snippet: .. In the present study, we used Illumina Hiseq ™ 2000 [ – ] sequencing to characterize the transcriptomes of eight samples, in order to provide the most comprehensive gene sequence resources for the blunt snout bream and to obtain differential expression (DE) genes related to growth and tolerance to hypoxia. ..

Sequencing:

Article Title: Transcriptome Analysis of Blunt Snout Bream (Megalobrama amblycephala) Reveals Putative Differential Expression Genes Related to Growth and Hypoxia
Article Snippet: .. In the present study, we used Illumina Hiseq ™ 2000 [ – ] sequencing to characterize the transcriptomes of eight samples, in order to provide the most comprehensive gene sequence resources for the blunt snout bream and to obtain differential expression (DE) genes related to growth and tolerance to hypoxia. ..

Article Title: An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data
Article Snippet: .. For 10 ccRCC samples, whole-genome sequencing and RNA sequencing were performed using HiSeq 2000, according to standard protocols recommended by Illumina. .. The mean sequencing depth for each sample was 65.9–223.0 ( Supplementary Table S1 and S2 ).

Mouse Assay:

Article Title: Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome
Article Snippet: .. In case of C57BL/6J mice and additional probes of CD1 OE, mRNA was sequenced on HiSeq-2000 (101-bp, paired end). .. Alignment of RNA-Seq reads using TopHat We analyzed the raw sequence data in fastq format as previously described [ ].

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  • 99
    Illumina Inc illumina hiseq 2000
    Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using <t>Illumina</t> <t>Hiseq</t> 2000 platform that generated 19089819 and 17312962 clean sequence respectively. (A) Venn diagram showing distribution of common and specific sRNA total sequence reads amongst the two libraries. (B) Venn diagram showing distribution of common and specific sRNA unique sequence reads amongst the two libraries. (C) Length distribution and frequency percent of sequences in HEK293 and HeLa mitochondrial sRNA libraries.
    Illumina Hiseq 2000, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 7571 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq 2000/product/Illumina Inc
    Average 99 stars, based on 7571 article reviews
    Price from $9.99 to $1999.99
    illumina hiseq 2000 - by Bioz Stars, 2020-07
    99/100 stars
      Buy from Supplier

    86
    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
    https://www.bioz.com/result/hiseq 2000 sequencing runs/product/Illumina Inc
    Average 86 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    hiseq 2000 sequencing runs - by Bioz Stars, 2020-07
    86/100 stars
      Buy from Supplier

    95
    Illumina Inc hiseq 2000 sequencer
    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina <t>HiSeq</t> 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).
    Hiseq 2000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 1338 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq 2000 sequencer/product/Illumina Inc
    Average 95 stars, based on 1338 article reviews
    Price from $9.99 to $1999.99
    hiseq 2000 sequencer - by Bioz Stars, 2020-07
    95/100 stars
      Buy from Supplier

    Image Search Results


    Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using Illumina Hiseq 2000 platform that generated 19089819 and 17312962 clean sequence respectively. (A) Venn diagram showing distribution of common and specific sRNA total sequence reads amongst the two libraries. (B) Venn diagram showing distribution of common and specific sRNA unique sequence reads amongst the two libraries. (C) Length distribution and frequency percent of sequences in HEK293 and HeLa mitochondrial sRNA libraries.

    Journal: PLoS ONE

    Article Title: Systematic Analysis of Small RNAs Associated with Human Mitochondria by Deep Sequencing: Detailed Analysis of Mitochondrial Associated miRNA

    doi: 10.1371/journal.pone.0044873

    Figure Lengend Snippet: Generation and analysis of sRNA sequences from mitochondria. sRNA library generated from mitochondria from HEK293 and HeLa were sequenced using Illumina Hiseq 2000 platform that generated 19089819 and 17312962 clean sequence respectively. (A) Venn diagram showing distribution of common and specific sRNA total sequence reads amongst the two libraries. (B) Venn diagram showing distribution of common and specific sRNA unique sequence reads amongst the two libraries. (C) Length distribution and frequency percent of sequences in HEK293 and HeLa mitochondrial sRNA libraries.

    Article Snippet: Bioinformatics Analysis of sRNA Libraries from Mitochondria All the 50 nt sequence tags generated from Illumina HiSeq 2000 went through data cleaning process which included getting rid of low quality tags.

    Techniques: Generated, Sequencing

    The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

    Journal: PLoS ONE

    Article Title: Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

    doi: 10.1371/journal.pone.0077910

    Figure Lengend Snippet: The growth of SRA data categorized by project types, and sequencing platforms. (A) The growth of the number of SRA studies categorized by project types. The number of studies are double that of the previous year. (B) The growth of the number of SRA experiments categorized by sequencing platforms. Over 200,000 experiments are submitted under approximately 14,000 studies. The experiments using Illumina HiSeq 2000 are dramatically increasing.

    Article Snippet: The top 3 of most used sequencer are Illumina HiSeq 2000, Illumina Genome Analyzer II, and 454 GS FLX Titanium (92,888, 42,274, and 19,463 experiments, respectively), and experiments with new sequencing platforms such as Complete Genomics, Helicos HeliScope, PacBio RS, and Ion Torrent PGM are also archived (1133, 437, 431, and 304 experiments, respectively).

    Techniques: Sequencing

    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

    Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).

    Journal: Genome Biology

    Article Title: Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

    doi: 10.1186/gb-2012-13-10-r92

    Figure Lengend Snippet: Performance summary of mRRBS . Ninety-six samples were processed using mRRBS and sequenced with eight lanes of Illumina HiSeq 2000 using 12 barcoded adapters per lane. (a) The total number of reads for each sample is shown 84 samples with > 5 million total reads were included in the subsequent comparisons. (b) Quartile plots of summary coverage depth from these samples. The minimum and maximum values are bounded by the light blue area in (b-d), while the darker blue area represents the interquartile range. The dark blue line indicates the median. (c,d) MspI in silico digestion of the hg19 genome produced a total of 1,124,739 fragments. (c) The percentage of fragments of each fragment size that were covered by at least one read. (d) The average coverage depth for fragments of each length. Genomic MspI-digested fragments longer than 300 bp were not included in the sequence alignment target, which partly contributes to the sharp drop in coverage at 300 bp in (c,d).

    Article Snippet: To evaluate the performance of the mRRBS protocol, we sequenced the 96 libraries using 8 lanes of an Illumina HiSeq 2000 sequencer with 12 libraries per lane, which produced a median of 11.3 million reads per library (Table and Figure ; Additional file ).

    Techniques: In Silico, Produced, Sequencing