hiseq2000 sequencer Search Results


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  • 96
    Illumina Inc hiseq2000 sequencer
    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the <t>Illumina</t> <t>HiSeq2000</t> platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
    Hiseq2000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 879 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq2000 sequencers
    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the <t>Illumina</t> <t>HiSeq2000</t> platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007
    Hiseq2000 Sequencers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq2000 sequencing
    Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for <t>HiSeq2000,</t> SOLiD 4, 5500xl SOLiD and Complete Genomics.
    Hiseq2000 Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc hiseq2000 1000 sequencer
    Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for <t>HiSeq2000,</t> SOLiD 4, 5500xl SOLiD and Complete Genomics.
    Hiseq2000 1000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Macrogen illumina hiseq2000 sequencer
    Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for <t>HiSeq2000,</t> SOLiD 4, 5500xl SOLiD and Complete Genomics.
    Illumina Hiseq2000 Sequencer, supplied by Macrogen, used in various techniques. Bioz Stars score: 91/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq2000 sequencer protocol
    Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for <t>HiSeq2000,</t> SOLiD 4, 5500xl SOLiD and Complete Genomics.
    Hiseq2000 Sequencer Protocol, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc hiseq2000 sequencing system
    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® <t>HiSeq2000</t> sequencing system.
    Hiseq2000 Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 434 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Illumina Inc illumina hiseq2000 2500 sequencers
    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® <t>HiSeq2000</t> sequencing system.
    Illumina Hiseq2000 2500 Sequencers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 93/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc hiseq2000 sequencing platform
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Hiseq2000 Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 744 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    LC Sciences illumina hiseq2000 2500 sequencer
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Illumina Hiseq2000 2500 Sequencer, supplied by LC Sciences, used in various techniques. Bioz Stars score: 91/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc hiseq2000 dna sequencers
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Hiseq2000 Dna Sequencers, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc hiseq2000 dna sequencer
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Hiseq2000 Dna Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Hokkaido System Science Co hiseq2000 sequencing system
    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina <t>HiSeq2000</t> sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .
    Hiseq2000 Sequencing System, supplied by Hokkaido System Science Co, used in various techniques. Bioz Stars score: 90/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq2000 sequencing machine
    Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a <t>HiSeq2000</t> sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.
    Hiseq2000 Sequencing Machine, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 43 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/hiseq2000 sequencing machine/product/Illumina Inc
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    91
    Macrogen illumina hiseq2000 sequencing
    Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a <t>HiSeq2000</t> sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.
    Illumina Hiseq2000 Sequencing, supplied by Macrogen, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Illumina Inc hiseq2000 sequence analyzer
    Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a <t>HiSeq2000</t> sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.
    Hiseq2000 Sequence Analyzer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc next generation hiseq2000 sequencer
    Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina <t>HiSeq2000</t> next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.
    Next Generation Hiseq2000 Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc hiseq2000 gaiix sequencer
    Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina <t>HiSeq2000</t> next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.
    Hiseq2000 Gaiix Sequencer, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Illumina Inc illumina hiseq2000 sequencing
    The circulating miRNAs signatures identified by <t>Illumina</t> <t>Hiseq2000</t> sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).
    Illumina Hiseq2000 Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 615 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/illumina hiseq2000 sequencing/product/Illumina Inc
    Average 94 stars, based on 615 article reviews
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    Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

    Journal: eLife

    Article Title: Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

    doi: 10.7554/eLife.11888

    Figure Lengend Snippet: Taxonomic classification of bacterioplankton metagenomes Sampling: Surface seawater samples were taken at the North Sea island Helgoland between the main island and the minor island 'Düne' (station 'Kabeltonne', 54°11.03' N, 7°54.00' E) and processed in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Biomass of free-living bacteria was harvested on 0.2 µm pore sized filters after pre-filtration with 10 µm and 3 µm pore sized filters to remove large debris and particle-associated bacteria. Sequencing: Community DNA was extracted and sequenced; 2009 samples were sequenced on the 454 FLX Ti platform, and 2010-2012 samples on the Illumina HiSeq2000 platform (16 metagenomes in total). Reads were assembled using Newbler (2009) or a combination of SOAPdenovo and Newbler (2010-2012) and the resulting contigs were taxonomically classified ( Supplementary file 9 ). Visualization: The resulting metagenome contigs are visualized as bubbles with radii that are proportional to their lengths and colors that indicate their predicted taxomomic affiliations. These bubbles are drawn in planes that are defined by the contig's GC contents and coverage values. Colors are restricted to selected abundant taxa (see legend below) to highlight distinct clusters, mostly from the Bacteroidetes, Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria . Likewise only contigs are shown that exceed a minimum length of 2750 bp for pyrosequencing data (2009) and 15,000 bp for llumina data (2010-2012), respectively. Sparse contigs with very high coverage or GC contents below 20% or above 60% were also excluded from visualizations. The 16 metagenomes are shown arranged in order on yearly timescales that depict chlorophyll a contents as proxies for phytoplankton abundance. Metagenome sizes*: 2009-02-11: 49.1 Mbp / 2009-03-31: 44.9 Mbp / 2009-04-07: 52.7 Mbp / 2009-04-14: 96.0 Mbp / 2009-06-16: 29.8 Mbp / 2009-09-01: 79.2 Mbp 2010-03-03: 537.3 Mbp / 2010-04-08: 325.8 Mbp / 2010-05-04: 453.0 Mbp / 2010-05-18: 512.3 Mbp 2011-03-24: 629.1 Mbp / 2011-04-28: 541.8 Mbp / 2011-05-26: 604.0 Mbp 2012-03-08: 574.0 Mbp / 2012-04-16: 543.9 Mbp / 2012-05-10: 614.1 Mbp *sums of assembled bases DOI: http://dx.doi.org/10.7554/eLife.11888.007

    Article Snippet: Sequencing was performed on the Illumina HiSeq2000 sequencer using TruSeq SBS sequencing Kits, v3, following a 2x150 bp indexed run recipe.

    Techniques: Sampling, Filtration, Sequencing

    Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

    Journal: PLoS ONE

    Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

    doi: 10.1371/journal.pone.0066621

    Figure Lengend Snippet: Bases without coverage in different genomic regions. (a) Mean percentage of bases not covered across genomic elements. Bases covered with less than three reads were considered not covered. Note that reducing this threshold to 1 does not dramatically change the overall distribution of reads ( Figure S8 ). Error bars represent one standard deviation as obtained from analyzing all samples listed in Table 1 . DNA, LINE, Low complexity, LTR, RC, RNA, Satellite, Simple repeats and SINE are subcategories of Repeats (all). For better visibility, CpG islands, low complexity and simple repeats are plotted separately. (b) Visualization of read coverage for two exemplary genomic regions from patient sample MB24 by IGV for HiSeq2000, SOLiD 4, 5500xl SOLiD and Complete Genomics.

    Article Snippet: For HiSeq2000 sequencing, a PhiX kit v2 library (Illumina) was spiked into the libraries at a proportion of about 1% each.

    Techniques: Standard Deviation

    GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

    Journal: PLoS ONE

    Article Title: Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

    doi: 10.1371/journal.pone.0066621

    Figure Lengend Snippet: GC bias for each platform. Log2 base coverage in 1 kb windows versus GC content for HiSeq2000, SOLiD 4, 5500xl SOLiD, and Complete Genomics data. The first panel shows an overlay of all four technologies. The upper right panel shows HiSeq2000 only (blue), the lower left SOLiD 4 and 5500xl SOLiD (red and orange, respectively) , and the lower right Complete Genomics at downsampled 30x coverage (light green). Smoothed loess curves are fitted to each dataset to represent the local coverage trend. Exemplary data from patient sample MB24 is shown.

    Article Snippet: For HiSeq2000 sequencing, a PhiX kit v2 library (Illumina) was spiked into the libraries at a proportion of about 1% each.

    Techniques:

    Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® HiSeq2000 sequencing system.

    Journal: Scientific Reports

    Article Title: Loss-of-function uORF mutations in human malignancies

    doi: 10.1038/s41598-018-19201-8

    Figure Lengend Snippet: Target sets and workflow of the PCR-based, multiplex identifier-tagged deep sequencing approach. ( A ) Composition of the cancer sample set with numbers indicating sample sizes of investigated malignant entities: ALL – acute lymphoblastic leukemia, AML – acute myeloid leukemia, NHL – non-Hodgkin lymphoma, OS – osteosarcoma, CA – colon adenocarcinoma, CX – colon xenograft, LA – lung adenocarcinoma, LX – lung xenograft, MC – mammary carcinoma. ( B ) Composition of the target gene set consisting of indicated numbers of uORF-bearing tyrosine kinases 5 , previously validated proto-oncogenes 18 and genes post-transcriptionally induced in cancer cell lines 19 (see also Supplementary Table 1 ). ( C ) Flow chart displaying amplification and normalization steps allowing simultaneous deep sequencing of 404 uORF initiation sites of 132 target genes in 308 individual cancer samples. Briefly, genomic regions of uAUG targets were amplified individually from every cancer DNA (see also Supplementary Table 7 ). uAUG-specific amplicons of each cancer sample were pooled and labeled with cancer-specific MID-tags in a second round of PCR (see also Supplementary Table 8 ). After normalization and pooling of all MID-tagged amplicons, a deep sequencing library was generated and analyzed using the Illumina® HiSeq2000 sequencing system.

    Article Snippet: Deep sequencing was performed on an Illumina® HiSeq2000 sequencing system with the TruSeq SBS Kit v3 and the PE (paired-end) Cluster Kit v3, producing read lengths of 2 × 101 nucleotides on average.

    Techniques: Polymerase Chain Reaction, Multiplex Assay, Sequencing, Flow Cytometry, Amplification, Labeling, Generated

    —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina HiSeq2000 sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .

    Journal: Genome Biology and Evolution

    Article Title: Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae

    doi: 10.1093/gbe/evy219

    Figure Lengend Snippet: —Exon–intron structure revealed by genomic DNA sequences. OmHT04 is used as an example. ( A ) Gene tree. ( B ) The coverage of short-reads of Illumina HiSeq2000 sequencing along OmHT04 . ( C ) Dotplot of comparison between OmHT04 and its homolog from Medicago truncatula .

    Article Snippet: For RNA sequencing, tissue-specific libraries were constructed for each species, and the libraries were sequenced separately by using the Illumina HiSeq2000 sequencing platform.

    Techniques: Sequencing

    Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.

    Journal: Genome Biology

    Article Title: Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

    doi: 10.1186/gb-2011-12-11-r112

    Figure Lengend Snippet: Frequencies and context of sequencing errors and quality scores compared to observed error rates . The sugar beet sample (yellow) and the Arabidopsis sample (blue) were each sequenced together with PhiX DNA (red and green, respectively) on a HiSeq2000 sequencing instrument. PhiX DNA only (black) was sequenced on a GAIIx. (a) Sequence context of substitution errors. The frequency of neighboring bases one position upstream and downstream of an error position is displayed. Sequence triplets were summarized for all types of base substitutions at the central position (indicated by an 'e'). We counted reads spanning the triplet positions and ignored potential further substitution errors within the triplet sequence of the read. The frequency was determined by dividing the occurrence of a triplet containing a central substitution error by the occurrence of all triplets with the same marginal bases but variable central base. The display of triplets is ordered by increasing average frequency in the HiSeq data. (b) Frequency of base substitution errors. For each sample, the proportion of each substitution is indicated (ordered by increasing average frequency in the HiSeq samples). (c) Rates of insertions or deletions in homopolymer tracts normalized by homopolymer length. Homopolymers longer than seven bases were present only in the two plant samples. Homopolymers of length 16 to 19 in the Bv-95nt data and of length 26 to 29 in the At-100nt data were each covered by less than 50 reads. (d) Expected versus observed error rates. Expected error rates according to quality scores (Q) were calculated for Q = 2 to Q = 40 (solid diagonal line). For each sample the uniquely aligned bases were grouped by quality score, and the observed error rate was determined from the number of observed substitution errors for each Q separately.

    Article Snippet: Results We generated genomic paired-end reads of 2 × 95 nucleotides and 2 × 100 nucleotides on an Illumina HiSeq2000 sequencing machine and of 2 × 150 nucleotides on an Illumina GAIIx instrument (Table ).

    Techniques: Sequencing

    Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.

    Journal: BMC Genomics

    Article Title: Systematic analysis of palatal transcriptome to identify cleft palate genes within TGF?3-knockout mice alleles: RNA-Seq analysis of TGF?3 Mice

    doi: 10.1186/1471-2164-14-113

    Figure Lengend Snippet: Experimental workflow of the study. RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous, heterozygous, and wildtype) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer. Fastq files were uploaded to the server for quality control analysis of sequence reads using FastQC. There were no sequence manipulation processes performed for any fastq file, given that the quality score was high at both the 3 ′ and 5 ′ ends. All of the reads were mapped to the reference genome (mm9, built name NCBIM37) by using TopHat. Quantification of transcripts, statistics tests for differential expression, and detection of splice variants were performed using Cufflinks; quality assessments of biological and technical replicates were performed using CummeRbund; and pairwise comparisons of samples and differential expression of transcripts were analyzed using CuffDiff. Venn diagrams of all significantly altered (FC ≥ 2.0) transcripts were drawn using the R VennDiagram package [ 75 ]. CP related genes (n = 322) were extracted from human (OMIM) and mouse (MGI) genome databases. CP genes were classified based on their patterns of expression (n = 9) for each genotype and their heatmaps were generated using the R pheatmap package. Expression pattern groups of CP genes were uploaded to IPA software as datasets and core analyses were run to detect downstream effects: canonical pathways and biological functions relevant to sample datasets.

    Article Snippet: Analysis of RNA-seq data As outlined in the experimental workflow of our study (Figure ), RNA samples were extracted from mouse palatal tissues of TGFβ3 knockout mice (homozygous (−/−), heterozygous (+/−), and wildtype (+/+)) at three developmental stages (E14.5, E15.5, and E16.5); libraries were prepared, converted to cDNA, and sequenced by using the Illumina HiSeq2000 next generation sequencer.

    Techniques: Knock-Out, Mouse Assay, Sequencing, Expressing, Generated, Indirect Immunoperoxidase Assay, Software

    The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Journal: Scientific Reports

    Article Title: The plasma miR-125a, miR-361 and miR-133a are promising novel biomarkers for Late-Onset Hypogonadism

    doi: 10.1038/srep23531

    Figure Lengend Snippet: The circulating miRNAs signatures identified by Illumina Hiseq2000 sequencing. The length distribution and frequency percentages of the sequences identified in LOH ( a ) and control samples ( b ) RNA species (unique tags aligning) in LOH ( c ) and control samples ( d ) and RNA read counts (total tags aligning) in LOH samples ( e ) and control samples ( f ).

    Article Snippet: Using Illumina HiSeq2000 sequencing at discovery phase, and then two-step validated by reverse transcriptase polymerase chain reaction (RT-PCR) assays in verification phases.

    Techniques: Sequencing