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Status |
Public on Jul 27, 2017 |
Title |
Genome wide DRIP-seq in control knockdown HeLa cells |
Organism |
Homo sapiens |
Experiment type |
Other
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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.
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Overall design |
Input and IP for two replicates of a DRIP-seq experiment in HeLa cells treated with a control siRNA
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Contributor(s) |
Cimrich K, Hamperl S, Bocek M, Saldivar J |
Citation(s) |
28802045 |
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Submission date |
Jan 10, 2017 |
Last update date |
Sep 02, 2021 |
Contact name |
Karlene Anne Cimprich |
E-mail(s) |
cimprich@stanford.edu
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Organization name |
Stanford University
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Street address |
318 Campus Drive
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City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94025 |
Country |
USA |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (4)
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Relations |
BioProject |
PRJNA360822 |
SRA |
SRP096360 |