|
| Status |
Public on Feb 01, 2016 |
| Title |
GRO-seq - mES - 12hr KD, 7SK ASO rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ES cells
cell line: v6.5
gender: male
|
| Treatment protocol |
Cells were depleted of 7SK by nucleofecting antisense oligonucleotides for 12 hours.
|
| Growth protocol |
mES cells were grown on gelatin plates with serum and LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were isolated and run-on reactions performed as described previously (PMID: 24843027).
Run-on RNA (labeled with BrU) was isolated as previously describd (PMID: 24843027) and deep sequencing libraries generated.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
nascent RNA
|
| Data processing |
After demultiplexing, reads were stripped adaptors, mapped to a custon index of repetitive RNAs (PMID: 25411354), mapped to the mouse (mm9) genome using Bowtie2, and processed as previously described (PMID: 24843027)
Replicates #1 and #2 have 13nt, 5'end barcodes, Replicates #3 and #4 have 17nt 5'end barcodes which need to be removed before mapping.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of merged biological replicates split for positive and negative strand reads of GRO-seq read density
|
| |
|
| Submission date |
Sep 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Ryan Alexander Flynn |
| E-mail(s) |
raflynn@stanford.edu
|
| Organization name |
Stanford University
|
| Street address |
380 Roth Way, Room 265
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE69142 |
7SK-BAF axis controls pervasive transcription at enhancers [GRO-Seq] |
| GSE69143 |
7SK-BAF axis controls pervasive transcription at enhancers |
|
| Relations |
| BioSample |
SAMN04025633 |
| SRA |
SRX1177107 |
