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  • 99
    New England Biolabs ultra strand specific rna seq library prep kit
    Ultra Strand Specific Rna Seq Library Prep Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc stranded rna sequencing rna seq illumina libraries
    Stranded Rna Sequencing Rna Seq Illumina Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 90/100, based on 180 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc strand specific rna sequencing paired end mrna seq illumina libraries
    Taxonomic composition of the stool metatranscriptome after storage of the sample in <t>RNA</t> later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to <t>mRNA</t> sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample
    Strand Specific Rna Sequencing Paired End Mrna Seq Illumina Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 88/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Kapa Biosystems kapa stranded rna sequencing rna seq library preparation kit
    Taxonomic composition of the stool metatranscriptome after storage of the sample in <t>RNA</t> later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to <t>mRNA</t> sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample
    Kapa Stranded Rna Sequencing Rna Seq Library Preparation Kit, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 93/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche kapa stranded rna sequencing rna seq library preparation kit
    Taxonomic composition of the stool metatranscriptome after storage of the sample in <t>RNA</t> later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to <t>mRNA</t> sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample
    Kapa Stranded Rna Sequencing Rna Seq Library Preparation Kit, supplied by Roche, used in various techniques. Bioz Stars score: 94/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc mrna rna sequencing rna seq libraries
    Taxonomic composition of the stool metatranscriptome after storage of the sample in <t>RNA</t> later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to <t>mRNA</t> sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample
    Mrna Rna Sequencing Rna Seq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc rna sequencing strand specific rna seq libraries
    Pipeline for identifying intact transcripts in mouse sperm. a) Strategy to assemble the transcriptome from mouse testis and sperm. The reconstruction of transcriptome mainly contained four steps. i , we compared the successfully aligned long reads (LRs) with the Ref-seq annotation of mm10 and assembled the short reads (SRs) using StringTie (version 1.3.1c, parameters -c 10 -p 10) 79 . SRs from sperm and testis were assembled separately and the two assemblies were then merged using StringTie again (the “merge” mode). Peaks from CAGE and PAS-seq were defined by AS-peak 80 . ii , Select isoforms that can be supported by any splicing patterns in Ref-seq or SR assembly. It should be noticed that we did not impose any restriction at 5’ or 3’ end at this stage. iii , Correct the ends of isoforms by CAGE and PAS peaks. iv , Novel isoforms were defined by selecting LRs that are not supported by either Ref-seq or SR assembly. These isoforms must have CAGE and PAS peaks to support their ends. v , Final assembly contains well annotated intact <t>RNA</t> in sperm and testis. b) Two examples of novel transcript structures in sperm. From top to bottom, genomic location, Ref-seq, PacBio reads <t>Illumina</t> reads sequencing from mouse sperm. c) Venn diagrams showing the contribution of alternative transcription start site (TSS), alternative splicing, and alternative polyA sites (APA) to the isoforms that differ from Ref-seq.
    Rna Sequencing Strand Specific Rna Seq Libraries, 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 strand specific rna seq illumina libraries
    Pipeline for identifying intact transcripts in mouse sperm. a) Strategy to assemble the transcriptome from mouse testis and sperm. The reconstruction of transcriptome mainly contained four steps. i , we compared the successfully aligned long reads (LRs) with the Ref-seq annotation of mm10 and assembled the short reads (SRs) using StringTie (version 1.3.1c, parameters -c 10 -p 10) 79 . SRs from sperm and testis were assembled separately and the two assemblies were then merged using StringTie again (the “merge” mode). Peaks from CAGE and PAS-seq were defined by AS-peak 80 . ii , Select isoforms that can be supported by any splicing patterns in Ref-seq or SR assembly. It should be noticed that we did not impose any restriction at 5’ or 3’ end at this stage. iii , Correct the ends of isoforms by CAGE and PAS peaks. iv , Novel isoforms were defined by selecting LRs that are not supported by either Ref-seq or SR assembly. These isoforms must have CAGE and PAS peaks to support their ends. v , Final assembly contains well annotated intact <t>RNA</t> in sperm and testis. b) Two examples of novel transcript structures in sperm. From top to bottom, genomic location, Ref-seq, PacBio reads <t>Illumina</t> reads sequencing from mouse sperm. c) Venn diagrams showing the contribution of alternative transcription start site (TSS), alternative splicing, and alternative polyA sites (APA) to the isoforms that differ from Ref-seq.
    Strand Specific Rna Seq Illumina Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 86/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc strand nonspecific rna sequencing rna seq library preparation truseq rna sample prep kits v2
    Pipeline for identifying intact transcripts in mouse sperm. a) Strategy to assemble the transcriptome from mouse testis and sperm. The reconstruction of transcriptome mainly contained four steps. i , we compared the successfully aligned long reads (LRs) with the Ref-seq annotation of mm10 and assembled the short reads (SRs) using StringTie (version 1.3.1c, parameters -c 10 -p 10) 79 . SRs from sperm and testis were assembled separately and the two assemblies were then merged using StringTie again (the “merge” mode). Peaks from CAGE and PAS-seq were defined by AS-peak 80 . ii , Select isoforms that can be supported by any splicing patterns in Ref-seq or SR assembly. It should be noticed that we did not impose any restriction at 5’ or 3’ end at this stage. iii , Correct the ends of isoforms by CAGE and PAS peaks. iv , Novel isoforms were defined by selecting LRs that are not supported by either Ref-seq or SR assembly. These isoforms must have CAGE and PAS peaks to support their ends. v , Final assembly contains well annotated intact <t>RNA</t> in sperm and testis. b) Two examples of novel transcript structures in sperm. From top to bottom, genomic location, Ref-seq, PacBio reads <t>Illumina</t> reads sequencing from mouse sperm. c) Venn diagrams showing the contribution of alternative transcription start site (TSS), alternative splicing, and alternative polyA sites (APA) to the isoforms that differ from Ref-seq.
    Strand Nonspecific Rna Sequencing Rna Seq Library Preparation Truseq Rna Sample Prep Kits V2, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc comparative transcriptomic analyses illumina strand specific rna seq libraries
    Comparative gene expression analysis of HIP, BIP and pneumococci from in vitro biofilm and planktonic pneumococci. (A) Dot plot representation of the whole genome <t>transcriptomic</t> profile for blood- isolated pneumococci, BIP ( blue ) and heart-isolated pneumococci, HIP ( red ) showing the average normalized number of <t>RNA-seq</t> reads identified, i.e. gene expression levels mapping to each TIGR4 gene within the blood and the heart. Y-axis denotes normalized expression levels (RPKMs) whereas X-axis denotes location of the genes on the TIGR4 chromosome. Established virulence determinants with expression levels > 1000 RNA-seq reads (i.e. corresponding to top 10% of genes with highest expression levels) for BIP and HIP are indicated. (B) Dot plot representation of the differential gene expression profile for BIP and HIP spanning the TIGR4 genome. The fold changes are depicted as Log 2 (HIP/BIP). Y-axis denotes log fold changes in gene expression levels whereas X-axis denotes location of the genes on the TIGR4 chromosome. Important differentially up-regulated pneumococcal genes for BIP and HIP are indicated in blue and red respectively. Genes clustered near the X-axis are consistently expressed. (C) Curve plot representation of gene expression levels for genes encoding designated pneumococcal virulence determinants in the BIP, HIP, in vitro biofilm-, and in vitro planktonic- TIGR4 samples. Y-axis denotes normalized expression levels (i.e. RPKMs) whereas X-axis denotes individual nucleotide location (nt coordinates) on the TIGR4 chromosome. Two pooled BIP samples (5 mice per sample), three HIP samples, three in vitro biofilms and three in vitro planktonic pneumococci samples were tested.
    Comparative Transcriptomic Analyses Illumina Strand Specific Rna Seq Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc illumina s truseq stranded rna seq sample prep kit
    Comparative gene expression analysis of HIP, BIP and pneumococci from in vitro biofilm and planktonic pneumococci. (A) Dot plot representation of the whole genome <t>transcriptomic</t> profile for blood- isolated pneumococci, BIP ( blue ) and heart-isolated pneumococci, HIP ( red ) showing the average normalized number of <t>RNA-seq</t> reads identified, i.e. gene expression levels mapping to each TIGR4 gene within the blood and the heart. Y-axis denotes normalized expression levels (RPKMs) whereas X-axis denotes location of the genes on the TIGR4 chromosome. Established virulence determinants with expression levels > 1000 RNA-seq reads (i.e. corresponding to top 10% of genes with highest expression levels) for BIP and HIP are indicated. (B) Dot plot representation of the differential gene expression profile for BIP and HIP spanning the TIGR4 genome. The fold changes are depicted as Log 2 (HIP/BIP). Y-axis denotes log fold changes in gene expression levels whereas X-axis denotes location of the genes on the TIGR4 chromosome. Important differentially up-regulated pneumococcal genes for BIP and HIP are indicated in blue and red respectively. Genes clustered near the X-axis are consistently expressed. (C) Curve plot representation of gene expression levels for genes encoding designated pneumococcal virulence determinants in the BIP, HIP, in vitro biofilm-, and in vitro planktonic- TIGR4 samples. Y-axis denotes normalized expression levels (i.e. RPKMs) whereas X-axis denotes individual nucleotide location (nt coordinates) on the TIGR4 chromosome. Two pooled BIP samples (5 mice per sample), three HIP samples, three in vitro biofilms and three in vitro planktonic pneumococci samples were tested.
    Illumina S Truseq Stranded Rna Seq Sample Prep Kit, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 441 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc sequencing strand specific rna seq cdna library preparation
    Global <t>cDNA</t> read count distribution and Hfq levels in Y. pseudotuberculosis during growth under environmental and infection-relevant conditions. (A) Percentage of uniquely mapped reads of the virulence plasmid pYV obtained by <t>RNA-seq</t> of Y . pseudotuberculosis YPIII and YPIIIΔ crp cDNA libraries. Libraries were generated from TAP-treated (+TAP) rRNA depleted RNA obtained from cultures grown to exponential (E) or stationary (S) growth phase at 25°C (25) and 37°C (37) (for detailed statistics see S1 Dataset ). The data represent the mean ± SEM from three independent biological replicates and were analyzed with Student’s t-test. **: P
    Sequencing Strand Specific Rna Seq Cdna Library Preparation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 63 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc stranded mrna library prep
    Global <t>cDNA</t> read count distribution and Hfq levels in Y. pseudotuberculosis during growth under environmental and infection-relevant conditions. (A) Percentage of uniquely mapped reads of the virulence plasmid pYV obtained by <t>RNA-seq</t> of Y . pseudotuberculosis YPIII and YPIIIΔ crp cDNA libraries. Libraries were generated from TAP-treated (+TAP) rRNA depleted RNA obtained from cultures grown to exponential (E) or stationary (S) growth phase at 25°C (25) and 37°C (37) (for detailed statistics see S1 Dataset ). The data represent the mean ± SEM from three independent biological replicates and were analyzed with Student’s t-test. **: P
    Stranded Mrna Library Prep, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 99/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa smarter universal low input dna seq kit
    Global <t>cDNA</t> read count distribution and Hfq levels in Y. pseudotuberculosis during growth under environmental and infection-relevant conditions. (A) Percentage of uniquely mapped reads of the virulence plasmid pYV obtained by <t>RNA-seq</t> of Y . pseudotuberculosis YPIII and YPIIIΔ crp cDNA libraries. Libraries were generated from TAP-treated (+TAP) rRNA depleted RNA obtained from cultures grown to exponential (E) or stationary (S) growth phase at 25°C (25) and 37°C (37) (for detailed statistics see S1 Dataset ). The data represent the mean ± SEM from three independent biological replicates and were analyzed with Student’s t-test. **: P
    Smarter Universal Low Input Dna Seq Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 98/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Taxonomic composition of the stool metatranscriptome after storage of the sample in RNA later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to mRNA sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample

    Journal: BMC Genomics

    Article Title: Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation

    doi: 10.1186/s12864-015-1694-y

    Figure Lengend Snippet: Taxonomic composition of the stool metatranscriptome after storage of the sample in RNA later or RNA Protect for up to 6 days in comparison to snap-frozen controls. Kraken was used to assign taxonomic labels to mRNA sequencing reads on the family level. ( a ) Absolute counts assigned to each family and ( b ) relative abundance of the families within each sample

    Article Snippet: Library construction and strand specific RNA sequencing Paired-end mRNA Seq Illumina libraries were constructed with the Script Seq Illumina Kit.

    Techniques: Sequencing

    Comparison of transcript abundance determined by qRT-PCR and Illlumina sequencing in mRNA extracted from stool. Samples were conserved in RNA Later or RNA Protect and stored at RT or 4 °C for the indicated time. Relative expression values obtained by RNA sequencing and qRT-PCR are shown for the external spikes sFGFP ( a ) and mCherry ( b )

    Journal: BMC Genomics

    Article Title: Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation

    doi: 10.1186/s12864-015-1694-y

    Figure Lengend Snippet: Comparison of transcript abundance determined by qRT-PCR and Illlumina sequencing in mRNA extracted from stool. Samples were conserved in RNA Later or RNA Protect and stored at RT or 4 °C for the indicated time. Relative expression values obtained by RNA sequencing and qRT-PCR are shown for the external spikes sFGFP ( a ) and mCherry ( b )

    Article Snippet: Library construction and strand specific RNA sequencing Paired-end mRNA Seq Illumina libraries were constructed with the Script Seq Illumina Kit.

    Techniques: Quantitative RT-PCR, Sequencing, Expressing, RNA Sequencing Assay

    Stability of transcripts from spike-ins and indigenous targets in stool mRNA for up to 15 days. Absolute copy numbers of the spikes sFGFP ( a ) and mCherry ( b ) and of the two indigenous targets 23S rRNA gene ( c ) and GAPDH gene ( d ) as determined by quantitative RT-PCR in stool samples. Samples were stored in RNA Later at room temperature (red graph) or at 4 °C (blue graph) or in RNA Protect at RT (black graph)

    Journal: BMC Genomics

    Article Title: Stool metatranscriptomics: A technical guideline for mRNA stabilisation and isolation

    doi: 10.1186/s12864-015-1694-y

    Figure Lengend Snippet: Stability of transcripts from spike-ins and indigenous targets in stool mRNA for up to 15 days. Absolute copy numbers of the spikes sFGFP ( a ) and mCherry ( b ) and of the two indigenous targets 23S rRNA gene ( c ) and GAPDH gene ( d ) as determined by quantitative RT-PCR in stool samples. Samples were stored in RNA Later at room temperature (red graph) or at 4 °C (blue graph) or in RNA Protect at RT (black graph)

    Article Snippet: Library construction and strand specific RNA sequencing Paired-end mRNA Seq Illumina libraries were constructed with the Script Seq Illumina Kit.

    Techniques: Quantitative RT-PCR

    Pipeline for identifying intact transcripts in mouse sperm. a) Strategy to assemble the transcriptome from mouse testis and sperm. The reconstruction of transcriptome mainly contained four steps. i , we compared the successfully aligned long reads (LRs) with the Ref-seq annotation of mm10 and assembled the short reads (SRs) using StringTie (version 1.3.1c, parameters -c 10 -p 10) 79 . SRs from sperm and testis were assembled separately and the two assemblies were then merged using StringTie again (the “merge” mode). Peaks from CAGE and PAS-seq were defined by AS-peak 80 . ii , Select isoforms that can be supported by any splicing patterns in Ref-seq or SR assembly. It should be noticed that we did not impose any restriction at 5’ or 3’ end at this stage. iii , Correct the ends of isoforms by CAGE and PAS peaks. iv , Novel isoforms were defined by selecting LRs that are not supported by either Ref-seq or SR assembly. These isoforms must have CAGE and PAS peaks to support their ends. v , Final assembly contains well annotated intact RNA in sperm and testis. b) Two examples of novel transcript structures in sperm. From top to bottom, genomic location, Ref-seq, PacBio reads Illumina reads sequencing from mouse sperm. c) Venn diagrams showing the contribution of alternative transcription start site (TSS), alternative splicing, and alternative polyA sites (APA) to the isoforms that differ from Ref-seq.

    Journal: bioRxiv

    Article Title: Single-molecule long-read sequencing reveals a conserved selection mechanism determining intact long RNA and miRNA profiles in sperm

    doi: 10.1101/2020.05.28.122382

    Figure Lengend Snippet: Pipeline for identifying intact transcripts in mouse sperm. a) Strategy to assemble the transcriptome from mouse testis and sperm. The reconstruction of transcriptome mainly contained four steps. i , we compared the successfully aligned long reads (LRs) with the Ref-seq annotation of mm10 and assembled the short reads (SRs) using StringTie (version 1.3.1c, parameters -c 10 -p 10) 79 . SRs from sperm and testis were assembled separately and the two assemblies were then merged using StringTie again (the “merge” mode). Peaks from CAGE and PAS-seq were defined by AS-peak 80 . ii , Select isoforms that can be supported by any splicing patterns in Ref-seq or SR assembly. It should be noticed that we did not impose any restriction at 5’ or 3’ end at this stage. iii , Correct the ends of isoforms by CAGE and PAS peaks. iv , Novel isoforms were defined by selecting LRs that are not supported by either Ref-seq or SR assembly. These isoforms must have CAGE and PAS peaks to support their ends. v , Final assembly contains well annotated intact RNA in sperm and testis. b) Two examples of novel transcript structures in sperm. From top to bottom, genomic location, Ref-seq, PacBio reads Illumina reads sequencing from mouse sperm. c) Venn diagrams showing the contribution of alternative transcription start site (TSS), alternative splicing, and alternative polyA sites (APA) to the isoforms that differ from Ref-seq.

    Article Snippet: Illumina RNA sequencing Strand-specific RNA-seq libraries were constructed following the TruSeq RNA sample preparation protocol as previously described with modifications , .

    Techniques: Sequencing

    Comparative gene expression analysis of HIP, BIP and pneumococci from in vitro biofilm and planktonic pneumococci. (A) Dot plot representation of the whole genome transcriptomic profile for blood- isolated pneumococci, BIP ( blue ) and heart-isolated pneumococci, HIP ( red ) showing the average normalized number of RNA-seq reads identified, i.e. gene expression levels mapping to each TIGR4 gene within the blood and the heart. Y-axis denotes normalized expression levels (RPKMs) whereas X-axis denotes location of the genes on the TIGR4 chromosome. Established virulence determinants with expression levels > 1000 RNA-seq reads (i.e. corresponding to top 10% of genes with highest expression levels) for BIP and HIP are indicated. (B) Dot plot representation of the differential gene expression profile for BIP and HIP spanning the TIGR4 genome. The fold changes are depicted as Log 2 (HIP/BIP). Y-axis denotes log fold changes in gene expression levels whereas X-axis denotes location of the genes on the TIGR4 chromosome. Important differentially up-regulated pneumococcal genes for BIP and HIP are indicated in blue and red respectively. Genes clustered near the X-axis are consistently expressed. (C) Curve plot representation of gene expression levels for genes encoding designated pneumococcal virulence determinants in the BIP, HIP, in vitro biofilm-, and in vitro planktonic- TIGR4 samples. Y-axis denotes normalized expression levels (i.e. RPKMs) whereas X-axis denotes individual nucleotide location (nt coordinates) on the TIGR4 chromosome. Two pooled BIP samples (5 mice per sample), three HIP samples, three in vitro biofilms and three in vitro planktonic pneumococci samples were tested.

    Journal: PLoS Pathogens

    Article Title: Streptococcus pneumoniae in the heart subvert the host response through biofilm-mediated resident macrophage killing

    doi: 10.1371/journal.ppat.1006582

    Figure Lengend Snippet: Comparative gene expression analysis of HIP, BIP and pneumococci from in vitro biofilm and planktonic pneumococci. (A) Dot plot representation of the whole genome transcriptomic profile for blood- isolated pneumococci, BIP ( blue ) and heart-isolated pneumococci, HIP ( red ) showing the average normalized number of RNA-seq reads identified, i.e. gene expression levels mapping to each TIGR4 gene within the blood and the heart. Y-axis denotes normalized expression levels (RPKMs) whereas X-axis denotes location of the genes on the TIGR4 chromosome. Established virulence determinants with expression levels > 1000 RNA-seq reads (i.e. corresponding to top 10% of genes with highest expression levels) for BIP and HIP are indicated. (B) Dot plot representation of the differential gene expression profile for BIP and HIP spanning the TIGR4 genome. The fold changes are depicted as Log 2 (HIP/BIP). Y-axis denotes log fold changes in gene expression levels whereas X-axis denotes location of the genes on the TIGR4 chromosome. Important differentially up-regulated pneumococcal genes for BIP and HIP are indicated in blue and red respectively. Genes clustered near the X-axis are consistently expressed. (C) Curve plot representation of gene expression levels for genes encoding designated pneumococcal virulence determinants in the BIP, HIP, in vitro biofilm-, and in vitro planktonic- TIGR4 samples. Y-axis denotes normalized expression levels (i.e. RPKMs) whereas X-axis denotes individual nucleotide location (nt coordinates) on the TIGR4 chromosome. Two pooled BIP samples (5 mice per sample), three HIP samples, three in vitro biofilms and three in vitro planktonic pneumococci samples were tested.

    Article Snippet: RNA-seq and comparative transcriptomic analyses Illumina strand-specific RNA-seq libraries were constructed with the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per manufacturer’s protocol.

    Techniques: Expressing, In Vitro, Isolation, RNA Sequencing Assay, Mouse Assay

    Global cDNA read count distribution and Hfq levels in Y. pseudotuberculosis during growth under environmental and infection-relevant conditions. (A) Percentage of uniquely mapped reads of the virulence plasmid pYV obtained by RNA-seq of Y . pseudotuberculosis YPIII and YPIIIΔ crp cDNA libraries. Libraries were generated from TAP-treated (+TAP) rRNA depleted RNA obtained from cultures grown to exponential (E) or stationary (S) growth phase at 25°C (25) and 37°C (37) (for detailed statistics see S1 Dataset ). The data represent the mean ± SEM from three independent biological replicates and were analyzed with Student’s t-test. **: P

    Journal: PLoS Genetics

    Article Title: Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

    doi: 10.1371/journal.pgen.1005087

    Figure Lengend Snippet: Global cDNA read count distribution and Hfq levels in Y. pseudotuberculosis during growth under environmental and infection-relevant conditions. (A) Percentage of uniquely mapped reads of the virulence plasmid pYV obtained by RNA-seq of Y . pseudotuberculosis YPIII and YPIIIΔ crp cDNA libraries. Libraries were generated from TAP-treated (+TAP) rRNA depleted RNA obtained from cultures grown to exponential (E) or stationary (S) growth phase at 25°C (25) and 37°C (37) (for detailed statistics see S1 Dataset ). The data represent the mean ± SEM from three independent biological replicates and were analyzed with Student’s t-test. **: P

    Article Snippet: Strand-specific library preparation and Illumina sequencing Strand-specific RNA-seq cDNA library preparation and barcode introduction was based on RNA adapter ligation as described previously [ ], omitting double strand specific nuclease normalization (DSN).

    Techniques: Infection, Plasmid Preparation, RNA Sequencing Assay, Generated

    Global identification of mRNA transcriptional start sites (TSSs). (A) Visualization of RNA-seq (+/- TAP) based cDNA sequencing reads mapped to the YPIII rovA , hfq , katY and crp gene locus using the Artemis genome browser (Release 15.0.0). (B) The 5’-UTR repertoire. The distribution and frequency of the length of 5’-UTRs is given for all mRNAs of YPIII which start upstream of the annotated translational start site. More than 40% of all 5’-UTRs are 20–60 nt in length. (Inset) Sequence conservation at the TSSs. Sequence logo computed from 1151 unaligned TSS regions (TSS is located at position +1) showing nucleotide conservation around the TSSs. The initial nucleotide of transcripts (position +1) is dominated by purines while position -1 is dominated by pyrimidines. (C) Detected conserved sequence motifs in the -35 and -10 promotor region.

    Journal: PLoS Genetics

    Article Title: Transcriptomic Profiling of Yersinia pseudotuberculosis Reveals Reprogramming of the Crp Regulon by Temperature and Uncovers Crp as a Master Regulator of Small RNAs

    doi: 10.1371/journal.pgen.1005087

    Figure Lengend Snippet: Global identification of mRNA transcriptional start sites (TSSs). (A) Visualization of RNA-seq (+/- TAP) based cDNA sequencing reads mapped to the YPIII rovA , hfq , katY and crp gene locus using the Artemis genome browser (Release 15.0.0). (B) The 5’-UTR repertoire. The distribution and frequency of the length of 5’-UTRs is given for all mRNAs of YPIII which start upstream of the annotated translational start site. More than 40% of all 5’-UTRs are 20–60 nt in length. (Inset) Sequence conservation at the TSSs. Sequence logo computed from 1151 unaligned TSS regions (TSS is located at position +1) showing nucleotide conservation around the TSSs. The initial nucleotide of transcripts (position +1) is dominated by purines while position -1 is dominated by pyrimidines. (C) Detected conserved sequence motifs in the -35 and -10 promotor region.

    Article Snippet: Strand-specific library preparation and Illumina sequencing Strand-specific RNA-seq cDNA library preparation and barcode introduction was based on RNA adapter ligation as described previously [ ], omitting double strand specific nuclease normalization (DSN).

    Techniques: RNA Sequencing Assay, Sequencing