|
Status |
Public on Feb 01, 2016 |
Title |
7SK ChIRP-seq - HeLa - Input |
Sample type |
SRA |
|
|
Source name |
HeLa cells
|
Organism |
Homo sapiens |
Characteristics |
cell type: Cervical cancer cells cell line: HeLa gender: female
|
Treatment protocol |
All cells were fixed with 1% gluteraldehyde for 10 minutes at room temperature.
|
Growth protocol |
mES cells were grown on gelatin plates with serum and LIF. Human ES cells were grown on matrigel plates. HeLa cells were grown on untreated plates
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Lysates were produced from soncated cell material and 7SK snRNA enriched with antisense oligonucleotide enrichment. Libraries were prepared according to the standard ChIRP-seq protocol (PMID: 21963238)
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
Affinity purified genomic DNA processed data file: hg19_7SK_ChIRP-seq_HeLa_Input.bw
|
Data processing |
Library strategy: ChIRP-seq After demultiplexing, reads were stripped adaptors and mapped to the mouse (mm9) or human (hg19) genome using Bowtie2. Even and Odd datasets were merged as described previously (PMID:21963238) and visualized as bigWig files. Peaks from the merged datasets were called using MACS2. Genome_build: mm9 or hg19 Supplementary_files_format_and_content: bigWig files of merged (even and odd probe sets) 7SK ChIRP-seq read density
|
|
|
Submission date |
May 21, 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 |
GPL11154 |
Series (2) |
GSE69141 |
7SK-BAF axis controls pervasive transcription at enhancers [ChIRP-Seq] |
GSE69143 |
7SK-BAF axis controls pervasive transcription at enhancers |
|
Relations |
BioSample |
SAMN03704208 |
SRA |
SRX1036405 |