|
| Status |
Public on Apr 05, 2012 |
| Title |
RNA pol II ChIP-Seq parent control |
| Sample type |
SRA |
| |
|
| Source name |
HEK293, RNA pol II ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
shRNA: none
chip antibody: rabbit anti-pan CTD
growth protocol: Cells were grown in DMEM 10% FCS.
|
| Treatment protocol |
HEK293 cells were stably infected with lentiviruses expressing the respective shRNAs or uninfected parent control.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
IPs from 2 ug of cross-linked extract were immunoprecipitated and prepared for Illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18 cycles) with Illumina PE primers using Phusion DNA polymerase.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Chromatin IP against RNA pol II.
Rabbit anti-pan C-terminal heptad repeat domain (CTD) (detects phosphorylated and non-phosphorylated Pol II CTD; Schroeder et al. Genes Dev. 14:2435, 2000).
|
| Data processing |
Single-end 34 base reads (after removing barcodes) were mapped to the hg18 UCSC human genome (Mar. 2006) with Bowtie version 0.12.5.
Genome Build:
hg18_parent_293pa__FC6298G_8_ATT.wig.gz: hg18
|
| |
|
| Submission date |
Mar 08, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
David L. Bentley |
| E-mail(s) |
david.bentley@ucdenver.edu
|
| Organization name |
U. Colorado School of Medicine
|
| Department |
Biochemistry and Mol. Genetics
|
| Street address |
12801 E. 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE36185 |
mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription |
|
| Relations |
| SRA |
SRX128195 |
| BioSample |
SAMN00809674 |
