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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Two-step RNA sequencing identifies a tissue-specific landscape of sense/antisense transcription

ABSTRACT: We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by two step RNA sequencing. Screening and verification of non-annotated transcriptional units by different RNA-Seq protocols.

ORGANISM(S): Mus musculus

SUBMITTER: Robert Haesler

PROVIDER: E-GEOD-28207 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A tissue-specific landscape of sense/antisense transcription in the mouse intestine.

Klostermeier Ulrich C UC Barann Matthias M Wittig Michael M Häsler Robert R Franke Andre A Gavrilova Olga O Kreck Benjamin B Sina Christian C Schilhabel Markus B MB Schreiber Stefan S Rosenstiel Philip P

BMC genomics 20110610

<h4>Background</h4>The intestinal mucosa is characterized by complex metabolic and immunological processes driven highly dynamic gene expression programs. With the advent of next generation sequencing and its utilization for the analysis of the RNA sequence space, the level of detail on the global architecture of the transcriptome reached a new order of magnitude compared to microarrays.<h4>Results</h4>We report the ultra-deep characterization of the polyadenylated transcriptome in two closely r ...[more]

PMID: 21663663

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Architectural complexity of the polyadenylated intestinal transcriptome revealed by hybrid RNA sequencing

Project description:We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by a hybrid RNA-sequencing. We show that 90.72% of the polyA-derived unique reads map to known genes, but 9.28% of reads matched to nonannotated genomic regions. Screening and verification of non-annotated transcriptional units by different RNA-Seq protocols.

2011-01-06 | E-GEOD-21699 | biostudies-arrayexpress

Two-step RNA sequencing identifies a tissue-specific landscape of sense/antisense transcription

Project description:We report the complexity of the polyadenylated transcriptome of the mouse intestinal tract assessed by two step RNA sequencing.

2011-03-29 | GSE28207 | GEO

Altered antisense-to-sense transcript ratios in breast cancer: Sage-Seq

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2010-12-10 | E-GEOD-25291 | biostudies-arrayexpress

Characterization of Basal and Estrogen-Regulated Antisense Transcription in Breast Cancer Cells: Role in Regulating Sense Transcription

Project description:We have mined genomic data to define three classes of antisense transcription in MCF-7 cells based on where their antisense transcription termination sites reside relative to their cognate sense mRNA and lncRNA genes. These three classes differ in their response to estrogen treatment, the enrichment of a number of genomic features associated with active promoters (H3K4me3, RNA polymerase II, open chromatin architecture), and the biological functions of their cognate sense genes as analyzed by DAVID gene ontology. We further characterized two estrogen-regulated antisense transcripts arising from the MYC gene in MCF-7 cells, showing that these antisense transcripts are five-prime capped, three-prime polyadenylated, and localized to different compartments of the cell.

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Antisense Drugs Make Sense for Neurological Diseases.

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Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast [ChIP-seq]

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