|
| Status |
Public on Apr 05, 2012 |
| Title |
Dcp1a ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
HeLa, Dcp1a ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
shRNA: none
chip antibody: rabbit anti-Dcp1a
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 Dcp1a.
Rabbit anti-Dcp1a (Lykke-Andersen, J., and Wagner, E. Genes Dev 19, 351-361, 2005).
|
| 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_dcp1_hela.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 |
SRX128194 |
| BioSample |
SAMN00809673 |
