Strand-specific RNA-seq analysis of three streptomycetes
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ABSTRACT:
PROVIDER: PRJNA196870 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters. For each of the three species (S. coelicolor, S. avermitilis, S. venezuelae) two libraries were created. The first was a long-read library, where total RNA was depleted of rRNA. The second was a short read library, where total RNA was size selected (40-300 nucleotides) prior to library creation. The long-read library allowed the profiling of mRNAs and asRNAs, while the short-read library was enriched for small RNAs (sRNAs).
2013-08-01 | E-GEOD-46008 | biostudies-arrayexpress
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2012-12-21 | E-MTAB-2798 | biostudies-arrayexpress
Project description:This experiment is contains rat organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from animals of three different strains (Sprague-Dawley, BN/SsNHsd and F344/Cr1). This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
2012-12-21 | E-MTAB-2800 | biostudies-arrayexpress
Project description:This experiment is contains chicken organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from three different animals as biological replicates. This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
2012-12-21 | E-MTAB-2797 | biostudies-arrayexpress
Project description:Strand-specific massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a comprehensive computational pipeline for the comparison of library quality metrics from any RNA-Seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library construction protocols, including both published and our own novel methods. We found marked differences in complexity, strand-specificity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing each method’s performance and ease, we identify the dUTP second strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in any organism. Examination of 11 different strand-specific RNA-Seq libraries from 7 distinct methods; also 2 control non-strand-specific RNA-Seq libraries. To assess the performance of each strand-specific library in digital expression profiling, we compared them to reference expression measurements estimated from expression profiles using competitive hybridization of a mid-log RNA sample vs. genomic DNA using Agilent arrays.
2010-08-15 | E-GEOD-21739 | biostudies-arrayexpress
Project description:This experiment is contains mouse organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part (with the exception of heart) was sourced from animals from three different strains: C57BL/6, DBA/2J and CD1. (There is no data for heart from the C57BL/6 strain.) This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
2012-12-21 | E-MTAB-2801 | biostudies-arrayexpress
Project description:This experiment is contains rhesus macaque organism part samples and strand-specific RNA-seq data from experiment E-GEOD-41637 (https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-41637/), which aimed at assessing tissue-specific transcriptome variation across mammals, with chicken used as an outgroup in evolutionary analyses. Each organism part was sourced from three different animals as biological replicates. This data set was originally submitted to NCBI Gene Expression Omnibus under accession number GSE41637 (http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE41637) and later imported to ArrayExpress as E-GEOD-41637.
2012-12-21 | E-MTAB-2799 | biostudies-arrayexpress
Project description:We applied single-end strand-specific RNA-seq experiments to compare the abundance of natural antisense transcripts in Arabidopsis. Examination of 3 wild type (WT) organs, including leaves, inflorescences and siliques.
2013-12-23 | E-GEOD-49950 | biostudies-arrayexpress
Project description:Strand-specific massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a comprehensive computational pipeline for the comparison of library quality metrics from any RNA-Seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library construction protocols, including both published and our own novel methods. We found marked differences in complexity, strand-specificity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing each method’s performance and ease, we identify the dUTP second strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in any organism.
2010-08-15 | GSE21739 | GEO
Project description:Strand-specific RNA-seq analysis after Ssrp1 knockout in embryonic stem cells
| PRJNA655887 | ENA