deep sequencing Illumina Inc Search Results


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  • 77
    Illumina Inc multiplexed deep sequencing
    Multiplexed Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Illumina Inc pyrosequencing
    Scans of chloroquine selection (LGS-pyro) . Allele proportions (sensitive strain, AJ) in uncloned progeny of genetic crosses using AS/AJ SNPs <t>(pyrosequencing).</t> A . Genome-wide - AS-30CQ × AJ parasites surviving 1.5 (black, ■), 3 (blue, ♦), 10 (green, ▲) or 20 (orange, + ) mg CQ kg -1 day -1 . The positions of mutations in aat1 , PCHAS_031370 and ubp1 are indicated, and the proportions of the wild-type (AJ) base at these positions (as estimated by proportional sequencing [ 54 ]) are included. B . Chromosome 11 selection valley - parasites surviving 3 mg CQ kg -1 day -1 , with position of aat1 mutation indicated; AS-30CQ × AJ backcross (blue, ♦), AS-15MF × AJ backcross (red, ■). The region previously defined by classical genetic linkage analysis [ 20 ] is shown (gradient shaded green box).
    Pyrosequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 95/100, based on 1565 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc rna deep sequencing
    <t>MiTRAP</t> allows the selective co-purification of miRNAs with in vitro transcribed bait RNAs. ( A ) Scheme of the miTRAP procedure. In vitro transcribed bait RNAs comprising four MS2 stem-loops fused to the 3′end of bait transcripts were immobilized on amylose resin (light gray) via recombinant MBP-fused (dark gray) MS2-CP (white) protein. ( B ) Scheme of the used bait RNAs (upper panel). MS2: 120-nt-long control <t>RNA</t> encoded by the template vector; WT: wild type 3′UTR of the MYC mRNA; MUT: MYC-3′UTR with indicated point mutations (lower panel) in the overlapping MTS of the let-7-5p/miR-34-5p families. ( C ) Co-purification of miRNAs was determined by qRT-PCR and assessed by the miTRAP ratio that indicates the input normalized abundance of miRNAs in the miTRAP eluates (upper panel). MiTRAP ratios of indicated miRNAs were determined on co-purification with depicted RNA baits (B) from U2OS cell lysates. Ratios were determined by qRT-PCR using miRNA-specific TaqMan probes. Note that MYC-regulatory miRNAs of the let-7-5p and miR-34-5p families are selectively co-purified with the MYC-3′UTR bait RNA, but not the mutant 3′UTR or MS2 control transcript. MiTRAP ratios for the WT 3′UTR bait are two orders of magnitude (note logarithmic scale) above controls. Error bars indicate standard deviation (s.d.) of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P ≤ 0.05. ( D ) Western blot analysis of indicated proteins isolated from U2OS input fractions or co-purified with MBP–MS2BP-coated amylose resin (BC), the MS2 control transcript (MS2), the WT or point mutated (MUT) MYC-3′UTR, respectively. TUBA4A served as negative control for unspecific binding, whereas MBP–MS2BP indicates equal loading of the resin. Retrieval of bait RNAs was monitored by urea PAGE and Syto60-staining of nucleic acids (lower panel). ( E, F ) Co-purification of the indicated miRNAs with the WT ZEB2-3′UTR or the MS2 control bait (MS2) from MCF7 cell lysates (E) or short let-7d-5p or miR-34a-5p antisense (as) bait transcripts from U2OS cell lysates (F) was monitored as described in (C). Error bars indicate s.d. of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P
    Rna Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 291 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Illumina Inc miseq deep sequencing system
    <t>MiTRAP</t> allows the selective co-purification of miRNAs with in vitro transcribed bait RNAs. ( A ) Scheme of the miTRAP procedure. In vitro transcribed bait RNAs comprising four MS2 stem-loops fused to the 3′end of bait transcripts were immobilized on amylose resin (light gray) via recombinant MBP-fused (dark gray) MS2-CP (white) protein. ( B ) Scheme of the used bait RNAs (upper panel). MS2: 120-nt-long control <t>RNA</t> encoded by the template vector; WT: wild type 3′UTR of the MYC mRNA; MUT: MYC-3′UTR with indicated point mutations (lower panel) in the overlapping MTS of the let-7-5p/miR-34-5p families. ( C ) Co-purification of miRNAs was determined by qRT-PCR and assessed by the miTRAP ratio that indicates the input normalized abundance of miRNAs in the miTRAP eluates (upper panel). MiTRAP ratios of indicated miRNAs were determined on co-purification with depicted RNA baits (B) from U2OS cell lysates. Ratios were determined by qRT-PCR using miRNA-specific TaqMan probes. Note that MYC-regulatory miRNAs of the let-7-5p and miR-34-5p families are selectively co-purified with the MYC-3′UTR bait RNA, but not the mutant 3′UTR or MS2 control transcript. MiTRAP ratios for the WT 3′UTR bait are two orders of magnitude (note logarithmic scale) above controls. Error bars indicate standard deviation (s.d.) of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P ≤ 0.05. ( D ) Western blot analysis of indicated proteins isolated from U2OS input fractions or co-purified with MBP–MS2BP-coated amylose resin (BC), the MS2 control transcript (MS2), the WT or point mutated (MUT) MYC-3′UTR, respectively. TUBA4A served as negative control for unspecific binding, whereas MBP–MS2BP indicates equal loading of the resin. Retrieval of bait RNAs was monitored by urea PAGE and Syto60-staining of nucleic acids (lower panel). ( E, F ) Co-purification of the indicated miRNAs with the WT ZEB2-3′UTR or the MS2 control bait (MS2) from MCF7 cell lysates (E) or short let-7d-5p or miR-34a-5p antisense (as) bait transcripts from U2OS cell lysates (F) was monitored as described in (C). Error bars indicate s.d. of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P
    Miseq Deep Sequencing System, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 14 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    86
    Illumina Inc hiseq2000 deep sequencing instrument
    Sequenced reads and the distribution of reads. The <t>Illumina</t> <t>Hiseq</t> 2000 sequencing of the microRNAs obtained from the sera of patients in the control group, carrier group, and CHB group, produced 9,364,754,10,491,694, and 7,896,608 raw-reads, respectively, which, after extensive preprocessing and quality control, were reduced to 459,890,859,216, and 494,523 clean reads (Fig. 2A–C). All the distribution of reads of 16–30 nt length is presented in Fig. 2D.
    Hiseq2000 Deep Sequencing Instrument, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc 454 pyrosequencing
    Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and <t>454-pyrosequencing</t> techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].
    454 Pyrosequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 669 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    81
    Illumina Inc deep sequencing platform illumina hiseq
    Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and <t>454-pyrosequencing</t> techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].
    Deep Sequencing Platform Illumina Hiseq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 81/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Illumina Inc 464 pyrosequencing
    Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and <t>454-pyrosequencing</t> techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].
    464 Pyrosequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Illumina Inc next generation amplicon deep sequencing
    Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and <t>454-pyrosequencing</t> techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].
    Next Generation Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Illumina Inc 16s rrna deep sequencing
    Microbiota composition of shed leech mucus obtained through Illumina sequencing of the V3-V4 hypervariable region of <t>16S</t> <t>rRNA</t> gene. (A) The relative abundance of total reads, following quality control, within phyla. (B) The relative abundance of reads, comprising ≥2% of total reads, of genera housed within Proteobacteria. * Indicates previously described within the leech (Worthen et al., 2006 ; Kikuchi et al., 2009 ). (C) The relative abundance of reads, comprising ≥1% of total reads, of genera housed within Bacteroidetes.
    16s Rrna Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 85/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Thermo Fisher 454 pyrosequencing
    Microbiota composition of shed leech mucus obtained through Illumina sequencing of the V3-V4 hypervariable region of <t>16S</t> <t>rRNA</t> gene. (A) The relative abundance of total reads, following quality control, within phyla. (B) The relative abundance of reads, comprising ≥2% of total reads, of genera housed within Proteobacteria. * Indicates previously described within the leech (Worthen et al., 2006 ; Kikuchi et al., 2009 ). (C) The relative abundance of reads, comprising ≥1% of total reads, of genera housed within Bacteroidetes.
    454 Pyrosequencing, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Illumina Inc gaii ultra deep sequencing platform
    Microbiota composition of shed leech mucus obtained through Illumina sequencing of the V3-V4 hypervariable region of <t>16S</t> <t>rRNA</t> gene. (A) The relative abundance of total reads, following quality control, within phyla. (B) The relative abundance of reads, comprising ≥2% of total reads, of genera housed within Proteobacteria. * Indicates previously described within the leech (Worthen et al., 2006 ; Kikuchi et al., 2009 ). (C) The relative abundance of reads, comprising ≥1% of total reads, of genera housed within Bacteroidetes.
    Gaii Ultra Deep Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Illumina Inc hiseq deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Hiseq Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 23 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Illumina Inc amplicon deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Amplicon Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 96 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc ultra deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Ultra Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Illumina Inc ngs deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Ngs Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 80/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Illumina Inc amplification deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Amplification Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 79/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Illumina Inc deep sequencing by synthesis sbs technology
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Deep Sequencing By Synthesis Sbs Technology, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc gls flx pyrosequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Gls Flx Pyrosequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc sbs deep sequencing platform
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Sbs Deep Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    75
    Illumina Inc unigenes illumina deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Unigenes Illumina Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 75/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Illumina Inc multiamplicon targeted deep sequencing
    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) <t>HiSeq</t> analysis showed elevated transcription of CEACAM1 in <t>H5N1-infected</t> ATII cells (HD) when compared to uninfected cells (ND). *** p
    Multiamplicon Targeted Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 78/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    84
    Illumina Inc srna deep sequencing
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Srna Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc next generation deep sequencing
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Next Generation Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 78/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc deep sequencing rnaseq technologies
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Deep Sequencing Rnaseq Technologies, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 78/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Illumina Inc umass deep sequencing core
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Umass Deep Sequencing Core, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 96/100, based on 29 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Illumina Inc mrna deep sequencing
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Mrna Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 41 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc ultra deep sequencing capacity
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Ultra Deep Sequencing Capacity, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    82
    Illumina Inc illumina deep sequencing analysis
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Illumina Deep Sequencing Analysis, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 82/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Illumina Inc parallel deep sequencing platform
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Parallel Deep Sequencing Platform, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 77/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    Illumina Inc gyra deep sequencing
    Quantitative real-time PCR validation of differentially expressed miRNAs identified using <t>Illumina</t> <t>sRNA</t> deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.
    Gyra Deep Sequencing, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 83/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc illumina deep sequencing data
    SEWAL pipeline for sequence analysis. SEWAL currently reads qseq.txt files generated by the <t>Illumina</t> pipeline. SEWAL commands are shown in italics. File types are shown by white boxes. All files are tab-delimited text files with defined formatting. Inset graphic is a screenshot of the SEWAL interactive graphics window.
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    Image Search Results


    Scans of chloroquine selection (LGS-pyro) . Allele proportions (sensitive strain, AJ) in uncloned progeny of genetic crosses using AS/AJ SNPs (pyrosequencing). A . Genome-wide - AS-30CQ × AJ parasites surviving 1.5 (black, ■), 3 (blue, ♦), 10 (green, ▲) or 20 (orange, + ) mg CQ kg -1 day -1 . The positions of mutations in aat1 , PCHAS_031370 and ubp1 are indicated, and the proportions of the wild-type (AJ) base at these positions (as estimated by proportional sequencing [ 54 ]) are included. B . Chromosome 11 selection valley - parasites surviving 3 mg CQ kg -1 day -1 , with position of aat1 mutation indicated; AS-30CQ × AJ backcross (blue, ♦), AS-15MF × AJ backcross (red, ■). The region previously defined by classical genetic linkage analysis [ 20 ] is shown (gradient shaded green box).

    Journal: BMC Genomics

    Article Title: Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria

    doi: 10.1186/1471-2164-13-106

    Figure Lengend Snippet: Scans of chloroquine selection (LGS-pyro) . Allele proportions (sensitive strain, AJ) in uncloned progeny of genetic crosses using AS/AJ SNPs (pyrosequencing). A . Genome-wide - AS-30CQ × AJ parasites surviving 1.5 (black, ■), 3 (blue, ♦), 10 (green, ▲) or 20 (orange, + ) mg CQ kg -1 day -1 . The positions of mutations in aat1 , PCHAS_031370 and ubp1 are indicated, and the proportions of the wild-type (AJ) base at these positions (as estimated by proportional sequencing [ 54 ]) are included. B . Chromosome 11 selection valley - parasites surviving 3 mg CQ kg -1 day -1 , with position of aat1 mutation indicated; AS-30CQ × AJ backcross (blue, ♦), AS-15MF × AJ backcross (red, ■). The region previously defined by classical genetic linkage analysis [ 20 ] is shown (gradient shaded green box).

    Article Snippet: Abbreviations AAT1: amino acid transporter 1; ABC: ATP-binding cassette; CQ: chloroquine; CQ-R: chloroquine resistant: chloroquine resistance; CQ-hiR: high level chloroquine resistance; CRT: chloroquine resistance transporter; DV: digestive vacuole; LGS: linkage group selection; LGS-pyro: LGS analysed by pyrosequencing; LGS-Illumina: LGS analysed by quantitative Illumina whole-genome sequencing; Pgh-1: P-glycoprotein homologue-1; QTL: quantitative trait loci; SNP: single nucleotide polymorphism; TM: transmembrane; WGS: whole genome (re-)sequencing; WTSI: Wellcome Trust Sanger Institute.

    Techniques: Selection, Genome Wide, Sequencing, Mutagenesis

    CAM-MREs are actively repressed in stiff substrates. (a) Schematic for CAM sensor library. The Sensor-Seq lentiviral library ( Methods ) consisted of (1) mCherry upstream of one of the 97 CAM-MRE, and (2) GFP lacking any MRE (control). Numbered MREs indicate different MREs within one CAM 3’UTR, alternatively one MRE was cloned per CAM 3’UTR ( Supplementary Table 4 ). (b) Left, mCherry and GFP intensities in HUVECs infected with the lentiviral library at 3 kPa and 30 kPa, a negative control (no MRE), and a positive control (3 perfect MREs for miR-125, abundant in HUVECs 45 ). Density plots show relative intensity of cell distribution using contour lines. Each contour line represents 15% of probability (higher= lighter grey, lower=darker grey) to contain cells in each bin over total cells (10,000 cells). Sensor-seq library-infected HUVECs at 3 kPa and 30 kPa were sorted into 4 bins, as indicated, based on mCherry/GFP expression relative to controls. Cells in each bin were isolated and genotyped using specific Illumina primer for sequencing ( Methods ). Right, Bar graph shows the percentage of mCherry+ cells sorted in each bin from 4 experiments (mean +/− SEM, single experiments are represented by dots) (c) CIRCOS 46 graphical representation of CAM miRNA-MRE interactions. Right quadrants: EC miRNAs with putative SEED matching to CAM MREs sensors displaying differential gene expression between 3 kPa and 30 kPa, divided in two groups: expressed at 3 kPa compared to 30 kPa (black line, top right) and expressed at 30 kPa compared to 3 kPa (black line, bottom right). Left quadrants: CAM-sensors most suppressed at 30 kPa compared to 3 kPa (black line, bottom left) and vice versa (black line, top left). Color-coded boxes indicate the categorized bins in ( b) at which cells were isolated and genotyped for a specific CAM-Sensors. Lines indicate match between individual miRNA (SEED) and CAM MRE in each condition. Color code indicates the level of complementarity between miRNA SEED and MRE nucleotides. The internal circles show the respective CAM-RNAs (red) and proteins (green) log2 fold change at 3 kPa compared to 30 kPa and 30 kPa compared to 3 kPa ( Supplementary tables 5 – 6 ). Source data can be found in Supplemental Table 8 .

    Journal: Nature cell biology

    Article Title: microRNA-dependent regulation of biomechanical genes establishes tissue stiffness homeostasis

    doi: 10.1038/s41556-019-0272-y

    Figure Lengend Snippet: CAM-MREs are actively repressed in stiff substrates. (a) Schematic for CAM sensor library. The Sensor-Seq lentiviral library ( Methods ) consisted of (1) mCherry upstream of one of the 97 CAM-MRE, and (2) GFP lacking any MRE (control). Numbered MREs indicate different MREs within one CAM 3’UTR, alternatively one MRE was cloned per CAM 3’UTR ( Supplementary Table 4 ). (b) Left, mCherry and GFP intensities in HUVECs infected with the lentiviral library at 3 kPa and 30 kPa, a negative control (no MRE), and a positive control (3 perfect MREs for miR-125, abundant in HUVECs 45 ). Density plots show relative intensity of cell distribution using contour lines. Each contour line represents 15% of probability (higher= lighter grey, lower=darker grey) to contain cells in each bin over total cells (10,000 cells). Sensor-seq library-infected HUVECs at 3 kPa and 30 kPa were sorted into 4 bins, as indicated, based on mCherry/GFP expression relative to controls. Cells in each bin were isolated and genotyped using specific Illumina primer for sequencing ( Methods ). Right, Bar graph shows the percentage of mCherry+ cells sorted in each bin from 4 experiments (mean +/− SEM, single experiments are represented by dots) (c) CIRCOS 46 graphical representation of CAM miRNA-MRE interactions. Right quadrants: EC miRNAs with putative SEED matching to CAM MREs sensors displaying differential gene expression between 3 kPa and 30 kPa, divided in two groups: expressed at 3 kPa compared to 30 kPa (black line, top right) and expressed at 30 kPa compared to 3 kPa (black line, bottom right). Left quadrants: CAM-sensors most suppressed at 30 kPa compared to 3 kPa (black line, bottom left) and vice versa (black line, top left). Color-coded boxes indicate the categorized bins in ( b) at which cells were isolated and genotyped for a specific CAM-Sensors. Lines indicate match between individual miRNA (SEED) and CAM MRE in each condition. Color code indicates the level of complementarity between miRNA SEED and MRE nucleotides. The internal circles show the respective CAM-RNAs (red) and proteins (green) log2 fold change at 3 kPa compared to 30 kPa and 30 kPa compared to 3 kPa ( Supplementary tables 5 – 6 ). Source data can be found in Supplemental Table 8 .

    Article Snippet: For mRNA libraries, total RNA was treated with DNA-free DNase (Ambion) and 500 ng of treated RNA was used to prepare Lexogen QuantSeq 3′ mRNA-Seq FWD libraries for Illumina deep-sequencing according to the manufacturer’s protocols.

    Techniques: Chick Chorioallantoic Membrane Assay, Clone Assay, Infection, Negative Control, Positive Control, Expressing, Isolation, Sequencing

    MIR2911 is highly enriched in HS decoction and is delivered into mouse lungs. (A , B) The levels (sequencing reads) of plant miRNAs in HS (A) and HS decoction (B) detected by Illumina sequencing. (C) The concentrations of MIR2911 in HS and HS decoction determined by RT-qPCR. (D) Northern blotting analysis showing MIR2911 expression in 10 g of HS or 10 ml of HS decoction (final concentration: ∼0.2 g HS/ml). (E) MIR2911 kinetics in mouse plasma after administration of 500 μl of HS decoction (MIR2911 concentration: 0.12 nM) by gavage (0 h, n = 30; other time point, n = 6). (F) MIR2911 kinetics in mouse lung tissue after administration of 500 μl of HS decoction (MIR2911 concentration: 0.12 nM) by gavage ( n = 5). (G , H) The MIR2911 level in mouse plasma (G) and lung tissue (H) 3 days after drinking HS decoction (MIR2911 concentration: 0.06 nM) ( n = 5). (I , J) The MIR2911 kinetics in mouse plasma (I) and lung tissue (J) after administration of 100 pmol synthetic MIR2911 in 100 μl PBS by gavage ( n = 5). (K) Fluorescently labeled MIR2911 in mouse lung tissue 3 h after administration of 2 nmol synthetic, fluorescently labeled MIR2911 by gavage (representative images are shown). Note that labeled MIR2911 (green dots) rapidly accumulated in mouse lungs. * P

    Journal: Cell Research

    Article Title: Honeysuckle-encoded atypical microRNA2911 directly targets influenza A viruses

    doi: 10.1038/cr.2014.130

    Figure Lengend Snippet: MIR2911 is highly enriched in HS decoction and is delivered into mouse lungs. (A , B) The levels (sequencing reads) of plant miRNAs in HS (A) and HS decoction (B) detected by Illumina sequencing. (C) The concentrations of MIR2911 in HS and HS decoction determined by RT-qPCR. (D) Northern blotting analysis showing MIR2911 expression in 10 g of HS or 10 ml of HS decoction (final concentration: ∼0.2 g HS/ml). (E) MIR2911 kinetics in mouse plasma after administration of 500 μl of HS decoction (MIR2911 concentration: 0.12 nM) by gavage (0 h, n = 30; other time point, n = 6). (F) MIR2911 kinetics in mouse lung tissue after administration of 500 μl of HS decoction (MIR2911 concentration: 0.12 nM) by gavage ( n = 5). (G , H) The MIR2911 level in mouse plasma (G) and lung tissue (H) 3 days after drinking HS decoction (MIR2911 concentration: 0.06 nM) ( n = 5). (I , J) The MIR2911 kinetics in mouse plasma (I) and lung tissue (J) after administration of 100 pmol synthetic MIR2911 in 100 μl PBS by gavage ( n = 5). (K) Fluorescently labeled MIR2911 in mouse lung tissue 3 h after administration of 2 nmol synthetic, fluorescently labeled MIR2911 by gavage (representative images are shown). Note that labeled MIR2911 (green dots) rapidly accumulated in mouse lungs. * P

    Article Snippet: Plant MIR2911 is absorbed and delivered into the lungs in mice after administration of HS decoction or synthetic MIR2911 All the short RNA fragments ( < 30 nt) extracted from HS were analyzed using Illumina deep-sequencing technology.

    Techniques: Sequencing, Quantitative RT-PCR, Northern Blot, Expressing, Concentration Assay, Labeling

    DNA methylation changes with age in candidate genes related to obesity, MetS, and T2D. (A) Methylation of CpG site cg12782180 located in the TSS1500 of LEP with respect to age. (B) Methylation of CpG site cg08119452 located in the TSS1500 of OLFM4 with respect to age. (C) Methylation of CpG site cg05404236 located in the first exon of IRS2 with respect to age. (D) Methylation of CpG site cg24366557 located in the body of TFAP2B with respect to age. (E) Pyrosequencing validation of differential methylation with age identified by arrays. Scatter plot shows the overlay of age-associated methylation changes at CpG site cg14956327 ( DDO ) probed by the Illumina HM450 array (black dots) and pyrosequencing (green dots). Only children and adolescents samples were used in validation tests. The insert shows direct comparisons between the Illumina array and pyrosequencing validation.

    Journal: Clinical Epigenetics

    Article Title: An epigenetic map of age-associated autosomal loci in northern European families at high risk for the metabolic syndrome

    doi: 10.1186/s13148-015-0048-6

    Figure Lengend Snippet: DNA methylation changes with age in candidate genes related to obesity, MetS, and T2D. (A) Methylation of CpG site cg12782180 located in the TSS1500 of LEP with respect to age. (B) Methylation of CpG site cg08119452 located in the TSS1500 of OLFM4 with respect to age. (C) Methylation of CpG site cg05404236 located in the first exon of IRS2 with respect to age. (D) Methylation of CpG site cg24366557 located in the body of TFAP2B with respect to age. (E) Pyrosequencing validation of differential methylation with age identified by arrays. Scatter plot shows the overlay of age-associated methylation changes at CpG site cg14956327 ( DDO ) probed by the Illumina HM450 array (black dots) and pyrosequencing (green dots). Only children and adolescents samples were used in validation tests. The insert shows direct comparisons between the Illumina array and pyrosequencing validation.

    Article Snippet: The graph within Figure E also shows a direct comparison of 13 samples between the Illumina array and pyrosequencing validation.

    Techniques: DNA Methylation Assay, Methylation

    MiTRAP allows the selective co-purification of miRNAs with in vitro transcribed bait RNAs. ( A ) Scheme of the miTRAP procedure. In vitro transcribed bait RNAs comprising four MS2 stem-loops fused to the 3′end of bait transcripts were immobilized on amylose resin (light gray) via recombinant MBP-fused (dark gray) MS2-CP (white) protein. ( B ) Scheme of the used bait RNAs (upper panel). MS2: 120-nt-long control RNA encoded by the template vector; WT: wild type 3′UTR of the MYC mRNA; MUT: MYC-3′UTR with indicated point mutations (lower panel) in the overlapping MTS of the let-7-5p/miR-34-5p families. ( C ) Co-purification of miRNAs was determined by qRT-PCR and assessed by the miTRAP ratio that indicates the input normalized abundance of miRNAs in the miTRAP eluates (upper panel). MiTRAP ratios of indicated miRNAs were determined on co-purification with depicted RNA baits (B) from U2OS cell lysates. Ratios were determined by qRT-PCR using miRNA-specific TaqMan probes. Note that MYC-regulatory miRNAs of the let-7-5p and miR-34-5p families are selectively co-purified with the MYC-3′UTR bait RNA, but not the mutant 3′UTR or MS2 control transcript. MiTRAP ratios for the WT 3′UTR bait are two orders of magnitude (note logarithmic scale) above controls. Error bars indicate standard deviation (s.d.) of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P ≤ 0.05. ( D ) Western blot analysis of indicated proteins isolated from U2OS input fractions or co-purified with MBP–MS2BP-coated amylose resin (BC), the MS2 control transcript (MS2), the WT or point mutated (MUT) MYC-3′UTR, respectively. TUBA4A served as negative control for unspecific binding, whereas MBP–MS2BP indicates equal loading of the resin. Retrieval of bait RNAs was monitored by urea PAGE and Syto60-staining of nucleic acids (lower panel). ( E, F ) Co-purification of the indicated miRNAs with the WT ZEB2-3′UTR or the MS2 control bait (MS2) from MCF7 cell lysates (E) or short let-7d-5p or miR-34a-5p antisense (as) bait transcripts from U2OS cell lysates (F) was monitored as described in (C). Error bars indicate s.d. of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P

    Journal: Nucleic Acids Research

    Article Title: Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification)

    doi: 10.1093/nar/gku127

    Figure Lengend Snippet: MiTRAP allows the selective co-purification of miRNAs with in vitro transcribed bait RNAs. ( A ) Scheme of the miTRAP procedure. In vitro transcribed bait RNAs comprising four MS2 stem-loops fused to the 3′end of bait transcripts were immobilized on amylose resin (light gray) via recombinant MBP-fused (dark gray) MS2-CP (white) protein. ( B ) Scheme of the used bait RNAs (upper panel). MS2: 120-nt-long control RNA encoded by the template vector; WT: wild type 3′UTR of the MYC mRNA; MUT: MYC-3′UTR with indicated point mutations (lower panel) in the overlapping MTS of the let-7-5p/miR-34-5p families. ( C ) Co-purification of miRNAs was determined by qRT-PCR and assessed by the miTRAP ratio that indicates the input normalized abundance of miRNAs in the miTRAP eluates (upper panel). MiTRAP ratios of indicated miRNAs were determined on co-purification with depicted RNA baits (B) from U2OS cell lysates. Ratios were determined by qRT-PCR using miRNA-specific TaqMan probes. Note that MYC-regulatory miRNAs of the let-7-5p and miR-34-5p families are selectively co-purified with the MYC-3′UTR bait RNA, but not the mutant 3′UTR or MS2 control transcript. MiTRAP ratios for the WT 3′UTR bait are two orders of magnitude (note logarithmic scale) above controls. Error bars indicate standard deviation (s.d.) of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P ≤ 0.05. ( D ) Western blot analysis of indicated proteins isolated from U2OS input fractions or co-purified with MBP–MS2BP-coated amylose resin (BC), the MS2 control transcript (MS2), the WT or point mutated (MUT) MYC-3′UTR, respectively. TUBA4A served as negative control for unspecific binding, whereas MBP–MS2BP indicates equal loading of the resin. Retrieval of bait RNAs was monitored by urea PAGE and Syto60-staining of nucleic acids (lower panel). ( E, F ) Co-purification of the indicated miRNAs with the WT ZEB2-3′UTR or the MS2 control bait (MS2) from MCF7 cell lysates (E) or short let-7d-5p or miR-34a-5p antisense (as) bait transcripts from U2OS cell lysates (F) was monitored as described in (C). Error bars indicate s.d. of at least three independent analyses. Statistical significance was determined by Student’s t -test: * P

    Article Snippet: Library preparation and deep sequencing RNA prepared from total miTRAP eluates and 8% input RNA (500 ng) was used in the small RNA protocol with the TruSeq™ Small RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the instructions of the manufacturer.

    Techniques: Copurification, In Vitro, Recombinant, Plasmid Preparation, Quantitative RT-PCR, Purification, Mutagenesis, Standard Deviation, Western Blot, Isolation, Negative Control, Binding Assay, Polyacrylamide Gel Electrophoresis, Staining

    Identification of novel MYC-3′UTR-associating miRNAs by miTRAP. ( A ) Summary of miRBase-mapped miRNA reads determined from indicated libraries of three independent miTRAP experiments using the MYC-3′UTR as bait RNA. Ratio in lower panel represents the ratio of total miRNA counts of the MYC to the MS2 libraries. ( B ) Box plots show miTRAP ratios determined for reported MYC-regulatory miRNAs (let-7a-i/98-5p, miR-34a/c-5p) co-purifying with the MS2 control (MS2) or WT MYC-3′UTR in three independent analyses. MiTRAP ratios were determined by TMM-normalized CPM values (counts per million) of indicated miRNAs in the MS2 or WT libraries versus the TMM-normalized CPM values of the respective miRNAs in the input libraries. Statistical significance was determined by Student’s t -test: * P

    Journal: Nucleic Acids Research

    Article Title: Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification)

    doi: 10.1093/nar/gku127

    Figure Lengend Snippet: Identification of novel MYC-3′UTR-associating miRNAs by miTRAP. ( A ) Summary of miRBase-mapped miRNA reads determined from indicated libraries of three independent miTRAP experiments using the MYC-3′UTR as bait RNA. Ratio in lower panel represents the ratio of total miRNA counts of the MYC to the MS2 libraries. ( B ) Box plots show miTRAP ratios determined for reported MYC-regulatory miRNAs (let-7a-i/98-5p, miR-34a/c-5p) co-purifying with the MS2 control (MS2) or WT MYC-3′UTR in three independent analyses. MiTRAP ratios were determined by TMM-normalized CPM values (counts per million) of indicated miRNAs in the MS2 or WT libraries versus the TMM-normalized CPM values of the respective miRNAs in the input libraries. Statistical significance was determined by Student’s t -test: * P

    Article Snippet: Library preparation and deep sequencing RNA prepared from total miTRAP eluates and 8% input RNA (500 ng) was used in the small RNA protocol with the TruSeq™ Small RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the instructions of the manufacturer.

    Techniques:

    Histogram displaying the single nucleotide substitutions in the miRNAs seed region sequence when aligning un-annotated sRNAs tags with mature miRNAs from miRBase20.0. The x -axis represents the substitution type from genome to RNA (small RNA sequence). The y -axis represents the percentage comparing of the observed count of each type to the total count of all substitution types.

    Journal: International Journal of Molecular Sciences

    Article Title: Identification of MicroRNA for Intermuscular Bone Development in Blunt Snout Bream (Megalobrama amblycephala)

    doi: 10.3390/ijms160510686

    Figure Lengend Snippet: Histogram displaying the single nucleotide substitutions in the miRNAs seed region sequence when aligning un-annotated sRNAs tags with mature miRNAs from miRBase20.0. The x -axis represents the substitution type from genome to RNA (small RNA sequence). The y -axis represents the percentage comparing of the observed count of each type to the total count of all substitution types.

    Article Snippet: The reads of these miRNAs were ranged from 1 to 2,796,874, indicating that not only highly-expressed miRNAs, but also weakly-expressed miRNAs were identified by Illumina small RNA deep sequencing.

    Techniques: Sequencing

    Quantitative real-time PCR validation of differentially expressed miRNAs identified using Illumina sRNA deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.

    Journal: PLoS ONE

    Article Title: MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata

    doi: 10.1371/journal.pone.0136383

    Figure Lengend Snippet: Quantitative real-time PCR validation of differentially expressed miRNAs identified using Illumina sRNA deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.

    Article Snippet: Identification of conserved mature miRNAs in A . marmorata The Illumina sRNAs deep sequencing approach allows us to determine the relative abundance of various miRNA by calculating the sequencing frequency.

    Techniques: Real-time Polymerase Chain Reaction, Sequencing, Expressing, Quantitative RT-PCR

    Length distribution of sRNA sequences of A . marmorata in three libraries. Sequence length distribution of clean reads based on the abundance; the most abundant size class was 22 nt in three libraries, followed by 23 nt in FW and BW but 29 nt in SW.

    Journal: PLoS ONE

    Article Title: MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata

    doi: 10.1371/journal.pone.0136383

    Figure Lengend Snippet: Length distribution of sRNA sequences of A . marmorata in three libraries. Sequence length distribution of clean reads based on the abundance; the most abundant size class was 22 nt in three libraries, followed by 23 nt in FW and BW but 29 nt in SW.

    Article Snippet: Identification of conserved mature miRNAs in A . marmorata The Illumina sRNAs deep sequencing approach allows us to determine the relative abundance of various miRNA by calculating the sequencing frequency.

    Techniques: Sequencing

    Sequenced reads and the distribution of reads. The Illumina Hiseq 2000 sequencing of the microRNAs obtained from the sera of patients in the control group, carrier group, and CHB group, produced 9,364,754,10,491,694, and 7,896,608 raw-reads, respectively, which, after extensive preprocessing and quality control, were reduced to 459,890,859,216, and 494,523 clean reads (Fig. 2A–C). All the distribution of reads of 16–30 nt length is presented in Fig. 2D.

    Journal: PLoS ONE

    Article Title: A Serum MicroRNA Panel as Potential Biomarkers for Hepatocellular Carcinoma Related with Hepatitis B Virus

    doi: 10.1371/journal.pone.0107986

    Figure Lengend Snippet: Sequenced reads and the distribution of reads. The Illumina Hiseq 2000 sequencing of the microRNAs obtained from the sera of patients in the control group, carrier group, and CHB group, produced 9,364,754,10,491,694, and 7,896,608 raw-reads, respectively, which, after extensive preprocessing and quality control, were reduced to 459,890,859,216, and 494,523 clean reads (Fig. 2A–C). All the distribution of reads of 16–30 nt length is presented in Fig. 2D.

    Article Snippet: Global analysis of miRNAs by deep sequencing Illumina HiSeq 2000 sequencing of the miRNAs obtained from the sera of patients in the healthy control group, cirrhosis group and HCC group produced 9,364,754, 10,491,694, and 7,896,608 raw-reads, respectively, which, after extensive preprocessing and quality control, were reduced to 459,890, 859,216, and 494,523 clean reads ( , ).

    Techniques: Sequencing, Produced

    Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and 454-pyrosequencing techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].

    Journal: PLoS ONE

    Article Title: Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout

    doi: 10.1371/journal.pone.0121778

    Figure Lengend Snippet: Comparison of total number of sequenced bases (A), total number of contigs (B), number of long contigs (≥ 500 bp) (C), and average length of contigs (D) obtained from Illumina, Sanger-based, and 454-pyrosequencing techniques. Data on Sanger-based and 454-pyrosequencing techniques were obtained from Salem et. al [ 29 ].

    Article Snippet: Compared to Sanger based and 454-pyrosequencing, Illumina allowed more effective assembly of the transcriptome with tremendous increases in the total number of contigs, total number of long contigs ( > 500 bp), and average length of contigs.

    Techniques:

    Microbiota composition of shed leech mucus obtained through Illumina sequencing of the V3-V4 hypervariable region of 16S rRNA gene. (A) The relative abundance of total reads, following quality control, within phyla. (B) The relative abundance of reads, comprising ≥2% of total reads, of genera housed within Proteobacteria. * Indicates previously described within the leech (Worthen et al., 2006 ; Kikuchi et al., 2009 ). (C) The relative abundance of reads, comprising ≥1% of total reads, of genera housed within Bacteroidetes.

    Journal: Frontiers in Microbiology

    Article Title: Characterization of shed medicinal leech mucus reveals a diverse microbiota

    doi: 10.3389/fmicb.2014.00757

    Figure Lengend Snippet: Microbiota composition of shed leech mucus obtained through Illumina sequencing of the V3-V4 hypervariable region of 16S rRNA gene. (A) The relative abundance of total reads, following quality control, within phyla. (B) The relative abundance of reads, comprising ≥2% of total reads, of genera housed within Proteobacteria. * Indicates previously described within the leech (Worthen et al., 2006 ; Kikuchi et al., 2009 ). (C) The relative abundance of reads, comprising ≥1% of total reads, of genera housed within Bacteroidetes.

    Article Snippet: Mucus sampling Day 3 mucus (i.e., 3 days post shedding) was chosen for both the construction of a mucosal 16S rRNA clone library and Illumina 16S rRNA deep sequencing, as this time point corresponds to the peak of Aeromonas population size (Ott et al., ).

    Techniques: Sequencing

    Bacterial phylogeny from shed leech mucus . Molecular phylogenetic tree of 16S rRNA gene sequences amplified from adult H. verbana mucosal secretions. A MP analysis tree created from approximately 900 aligned nucleotides is shown. Significance values, represented in MP bootstrap and Bayesian PP (BS/PP), are indicated at respective nodes. A bolded branch with “BS/n.a.” significance value refers to a branch that was not statistically supported by Bayesian analysis. Branch lengths are measured in number of substitutions over the whole sequence. Representative 16S rRNA sequences obtained within shed mucus are in bold, with other sequences obtained from NCBI indicated by accession numbers. Previously described leech isolates obtained through study of the gut and bladder systems are indicated by an * (Worthen et al., 2006 ) or # (Kikuchi et al., 2009 ), respectively. Color blocks indicate the Class housing the representative sequences.

    Journal: Frontiers in Microbiology

    Article Title: Characterization of shed medicinal leech mucus reveals a diverse microbiota

    doi: 10.3389/fmicb.2014.00757

    Figure Lengend Snippet: Bacterial phylogeny from shed leech mucus . Molecular phylogenetic tree of 16S rRNA gene sequences amplified from adult H. verbana mucosal secretions. A MP analysis tree created from approximately 900 aligned nucleotides is shown. Significance values, represented in MP bootstrap and Bayesian PP (BS/PP), are indicated at respective nodes. A bolded branch with “BS/n.a.” significance value refers to a branch that was not statistically supported by Bayesian analysis. Branch lengths are measured in number of substitutions over the whole sequence. Representative 16S rRNA sequences obtained within shed mucus are in bold, with other sequences obtained from NCBI indicated by accession numbers. Previously described leech isolates obtained through study of the gut and bladder systems are indicated by an * (Worthen et al., 2006 ) or # (Kikuchi et al., 2009 ), respectively. Color blocks indicate the Class housing the representative sequences.

    Article Snippet: Mucus sampling Day 3 mucus (i.e., 3 days post shedding) was chosen for both the construction of a mucosal 16S rRNA clone library and Illumina 16S rRNA deep sequencing, as this time point corresponds to the peak of Aeromonas population size (Ott et al., ).

    Techniques: Amplification, Sequencing

    Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) HiSeq analysis showed elevated transcription of CEACAM1 in H5N1-infected ATII cells (HD) when compared to uninfected cells (ND). *** p

    Journal: Scientific Reports

    Article Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1

    doi: 10.1038/s41598-018-33605-6

    Figure Lengend Snippet: Upregulation of CEACAM1 in influenza virus-infected cells. ( A ) HiSeq analysis showed elevated transcription of CEACAM1 in H5N1-infected ATII cells (HD) when compared to uninfected cells (ND). *** p

    Article Snippet: Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.

    Techniques: Infection

    Human host gene expression profiles following HPAI H5N1 infection and apocynin treatment. Genes that were statistically upregulated (shown as red circles) or downregulated (shown as blue circles) were assessed in pairwise comparisons as indicated. Data are plotted as the mean FPKM of each gene obtained from HD or HA against a Log2 fold change compared to ND as ( A ) ND vs . HD or ( B ) ND vs . HA, or compared to HD as ( C ) HD vs . HA. ( D–H ) The number and overlap of genes in each pairwise comparison is illustrated by Venn diagrams. ND, uninfected cells treated with 1% DMSO vehicle control; HD and HA, cells infected with H5N1 at a MOI of 2 for 24 hours in the presence of 1% DMSO or 1 mM apocynin, respectively. Up; upregulated. Down; downregulated. FPKM; fragments per kilobase of exon per million fragments mapped. RNA samples were obtained from ATII cells isolated from the lung tissue of three donors. The full list of transcripts identified in the HiSeq analysis, as well as differentially regulated transcripts in the three experimental groups is presented in Table S1 .

    Journal: Scientific Reports

    Article Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1

    doi: 10.1038/s41598-018-33605-6

    Figure Lengend Snippet: Human host gene expression profiles following HPAI H5N1 infection and apocynin treatment. Genes that were statistically upregulated (shown as red circles) or downregulated (shown as blue circles) were assessed in pairwise comparisons as indicated. Data are plotted as the mean FPKM of each gene obtained from HD or HA against a Log2 fold change compared to ND as ( A ) ND vs . HD or ( B ) ND vs . HA, or compared to HD as ( C ) HD vs . HA. ( D–H ) The number and overlap of genes in each pairwise comparison is illustrated by Venn diagrams. ND, uninfected cells treated with 1% DMSO vehicle control; HD and HA, cells infected with H5N1 at a MOI of 2 for 24 hours in the presence of 1% DMSO or 1 mM apocynin, respectively. Up; upregulated. Down; downregulated. FPKM; fragments per kilobase of exon per million fragments mapped. RNA samples were obtained from ATII cells isolated from the lung tissue of three donors. The full list of transcripts identified in the HiSeq analysis, as well as differentially regulated transcripts in the three experimental groups is presented in Table S1 .

    Article Snippet: Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.

    Techniques: Expressing, Infection, Isolation

    Hiseq analysis of H5N1 influenza virus gene expression and validation of differential gene expression identified with HiSeq using qRT-PCR. The same RNA samples used for HiSeq analysis were also subjected to qRT-PCR analysis of ( A ) IL6 , ( B ) IFNB1 , ( C ) CXCL10 , ( D ) CCL5 , ( E ) SOCS1 and ( F ) SOCS3 mRNA expression in three experimental groups of ATII cells (ND, HD and HA). Fold-changes following qRT-PCR analysis were calculated using 2 −ΔΔCt method (right Y axis) normalized to β - actin and compared with the ND group. Data from HiSeq was calculated as Log2 fold-change (left Y axis) compared with the ND group. IFNB1 transcription was not detected in ND, therefore HiSeq IFNB1 data from HD and HA groups was expressed as FPKM. * p

    Journal: Scientific Reports

    Article Title: Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1

    doi: 10.1038/s41598-018-33605-6

    Figure Lengend Snippet: Hiseq analysis of H5N1 influenza virus gene expression and validation of differential gene expression identified with HiSeq using qRT-PCR. The same RNA samples used for HiSeq analysis were also subjected to qRT-PCR analysis of ( A ) IL6 , ( B ) IFNB1 , ( C ) CXCL10 , ( D ) CCL5 , ( E ) SOCS1 and ( F ) SOCS3 mRNA expression in three experimental groups of ATII cells (ND, HD and HA). Fold-changes following qRT-PCR analysis were calculated using 2 −ΔΔCt method (right Y axis) normalized to β - actin and compared with the ND group. Data from HiSeq was calculated as Log2 fold-change (left Y axis) compared with the ND group. IFNB1 transcription was not detected in ND, therefore HiSeq IFNB1 data from HD and HA groups was expressed as FPKM. * p

    Article Snippet: Human host gene expression following HPAI H5N1 virus (A/Chicken/Vietnam/0008/04) infection of primary ATII cells was analyzed using Illumina HiSeq deep sequencing.

    Techniques: Expressing, Quantitative RT-PCR

    Quantitative real-time PCR validation of differentially expressed miRNAs identified using Illumina sRNA deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.

    Journal: PLoS ONE

    Article Title: MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata

    doi: 10.1371/journal.pone.0136383

    Figure Lengend Snippet: Quantitative real-time PCR validation of differentially expressed miRNAs identified using Illumina sRNA deep sequencing. (A) Profile of sequencing frequencies for miRNAs in different salinities; (B) Profile of relative expression of miRNAs evaluated by qRT-PCR.

    Article Snippet: In order to clarify whether miRNAs play relevant roles in the osmoregulation of Anguilla marmorata , three sRNA libraries of A . marmorata during adjusting to three various salinities were sequenced by Illumina sRNA deep sequencing methods.

    Techniques: Real-time Polymerase Chain Reaction, Sequencing, Expressing, Quantitative RT-PCR

    Length distribution of sRNA sequences of A . marmorata in three libraries. Sequence length distribution of clean reads based on the abundance; the most abundant size class was 22 nt in three libraries, followed by 23 nt in FW and BW but 29 nt in SW.

    Journal: PLoS ONE

    Article Title: MicroRNA-Sequence Profiling Reveals Novel Osmoregulatory MicroRNA Expression Patterns in Catadromous Eel Anguilla marmorata

    doi: 10.1371/journal.pone.0136383

    Figure Lengend Snippet: Length distribution of sRNA sequences of A . marmorata in three libraries. Sequence length distribution of clean reads based on the abundance; the most abundant size class was 22 nt in three libraries, followed by 23 nt in FW and BW but 29 nt in SW.

    Article Snippet: In order to clarify whether miRNAs play relevant roles in the osmoregulation of Anguilla marmorata , three sRNA libraries of A . marmorata during adjusting to three various salinities were sequenced by Illumina sRNA deep sequencing methods.

    Techniques: Sequencing

    SEWAL pipeline for sequence analysis. SEWAL currently reads qseq.txt files generated by the Illumina pipeline. SEWAL commands are shown in italics. File types are shown by white boxes. All files are tab-delimited text files with defined formatting. Inset graphic is a screenshot of the SEWAL interactive graphics window.

    Journal: Nucleic Acids Research

    Article Title: SEWAL: an open-source platform for next-generation sequence analysis and visualization

    doi: 10.1093/nar/gkq661

    Figure Lengend Snippet: SEWAL pipeline for sequence analysis. SEWAL currently reads qseq.txt files generated by the Illumina pipeline. SEWAL commands are shown in italics. File types are shown by white boxes. All files are tab-delimited text files with defined formatting. Inset graphic is a screenshot of the SEWAL interactive graphics window.

    Article Snippet: We present here an open-source software package entitled SEWAL (S equence E volution W ith A daptive L andscapes) designed to analyze Illumina deep-sequencing data and display it in the form of interactive three-dimensional (3D) scatter plots.

    Techniques: Sequencing, Generated