|
| Status |
Public on Dec 11, 2015 |
| Title |
Lib131 |
| Sample type |
SRA |
| |
|
| Source name |
THP1, pLKO.1-PAF1 shRNA #1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP1
genotype/variation: PAF1 knockdown
chip antibody: Pol II (ser-5p) (Abcam, ab5131)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were constructed with 5 to 10 ng immunoprecipitated DNA. Samples were sequenced on HiSeq 2000 by following the manufactor's protocols. RNA libraries were prepared for sequencing using strand-specific protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw sequenced reads were mapped to reference genome hg19 using BWA with default settings through GALAXY.
ChIPseq peaks were called by SICER software with parameter settings as W=200,G=400, and FDR=0.001
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using rpkmforgenes.py developed by Sandberg.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each RNA-seq Sample; bedGraph files were generated for each ChIP-Seq sample.
|
| |
|
| Submission date |
Oct 12, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Roeder |
| E-mail(s) |
roeder@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE62171 |
RNA Polymerase II-associated factor 1 regulates the release and phosphorylation of paused RNA Polymerase II |
|
| Relations |
| SRA |
SRX1329041 |
| BioSample |
SAMN04160361 |
