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Series GSE93368 Query DataSets for GSE93368
Status Public on Jul 27, 2017
Title Genome wide DRIP-seq in control knockdown HeLa cells
Organism Homo sapiens
Experiment type Other
Summary We mapped the location of RNA:DNA hybrids in HeLa cells that had been knocked down with a control siRNA. We found that the levels of RNA:DNA hybrids around origins of replication (defined from data from Pretyk et al, Nat Commun 2016) strongly correlated to the directionality of transcription around these origins (defined from GRO-seq data from GEO dataset GSM1518913.) Specifically, in regions where the replication fork travels antiparallel (Head-On) to the direction of transcription we find elevated RNA:DNA hybrids, and in regions where the replication fork travels parallel to the direction of replication (Co-directional) we find reduced RNA:DNA hybrids. These results imply that the relative directions of replication and transcription have an effect on the levels of RNA:DNA hybrids across the genome.
 
Overall design Input and IP for two replicates of a DRIP-seq experiment in HeLa cells treated with a control siRNA
 
Contributor(s) Cimrich K, Hamperl S, Bocek M, Saldivar J
Citation(s) 28802045
Submission date Jan 10, 2017
Last update date Sep 02, 2021
Contact name Karlene Anne Cimprich
E-mail(s) cimprich@stanford.edu
Organization name Stanford University
Street address 318 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94025
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (4)
GSM2452072 S9.6 DRIP Seq_1
GSM2452073 HeLa input_1
GSM2668157 S9.6 DRIP Seq_2
Relations
BioProject PRJNA360822
SRA SRP096360

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
GSE93368_RAW.tar 546.8 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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