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Series GSE87607 Query DataSets for GSE87607
Status Public on Oct 22, 2019
Title R-loops promote antisense transcription across the mammalian genome
Organism Homo sapiens
Experiment type Other
Summary We report the correlation we found between R-loops and antisense trasncription initiation. Our in vitro data suggests that RNA pol II can initiate transcription off the displaced single stranded DNA from within the R-loop. Therefore we generated Chromatin associated RNA-seq with and without over-expressing RNaseH1 and RDIP-seq (the directional RNA-seq of the RNA moeity from within the S9.6 pull down R-loop) as well as RR-ChIP-seq (the directional RNA-seq of the RNA moeity from within the catalytically dead RNaseH1-GFP GFP pull down R-loop) and confirm the correlation in vivo. We also aligned our findings with ChrCAP-seq (which is is a library enriched for RNA polymerase II capped RNA using chromatin associated RNA as the initial source) and found that capped antisense RNA were sensitive to RNase H1 overexpression.
Overall design Examination of chromatin associated RNA of HeLa cells and capped RNA with and without over-expressing RNAseH1. Directional R-loop occupancy was conducted by 1) sequencing the RNA moeity of the R-loop fragments which were immunoprecipitated by mouse monoclonal S9.6 antibody and by 2) sequencing the RNA moeity of the RNA:DNA hybrids caught in a catalytically dead RNaseH1-GFP.
Contributor(s) Tan-Wong SM, Dhir S, Proudfoot NJ
Citation(s) 31679819
Submission date Oct 04, 2016
Last update date Aug 27, 2020
Contact name Nicholas Proudfoot
Organization name Sir William Dunn School of Pathology, University of Oxford
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3RE
Country United Kingdom
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (14)
GSM2335051 Replicate1,chrRNA-seq WildType
GSM2335052 Replicate1, chrRNA-seq RnaseH1_oversxpression
GSM3681017 Replicate2, chrRNA-seq WildType
BioProject PRJNA345371
SRA SRP090821

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE87607_RAW.tar 3.3 Gb (http)(custom) TAR (of BW, TXT)
GSE87607_RDIP_pRNH1-GFP.peaks.txt.gz 160.6 Kb (ftp)(http) TXT
GSE87607_RR-ChIP_D210N.peaks.txt.gz 231.0 Kb (ftp)(http) TXT
GSE87607_RR-ChIP_pRNH1-GFP.peaks.txt.gz 239 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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