|
| Status |
Public on Mar 09, 2012 |
| Title |
RNA Polymerase 2 ChIP-Seq mm9ES wt |
| Sample type |
SRA |
| |
|
| Source name |
mm9ES_wt_RNA Polymerase 2 ChIP-Seq
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: wild type
cell type: embryonic stem (ES) cells
chip antibody: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody
chip antibody vendor: Abcam
chip antibody cat. #: ab5095
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinking for all the cell types used was carried out for 3 mins in 1% formaldehyde. Crosslinked chromatin from 10^7 cells and 60mg of antibody was used for each immunoprecipitation. Purified DNA was subjected to end-repair and adapter ligation using a sample preparation kit from Illumina according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 6
processed data file: Ser2Pol2_mm9ES_wt_w1000s100.wig (available on Series records)
|
| Data processing |
Sequence reads were mapped to the hg18 or mm9 genomes as appropriate using the Illumina Genome Analyser Pipeline. Reads with less than two mismatches were not aligned.
Coverage was calculated in 1 Kb windows using a step of 100 nt across the genome.
|
| |
|
| Submission date |
Jan 25, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Brick |
| E-mail(s) |
brickkm@mail.nih.gov, kevbrick@gmail.com, brickkm@niddk.nih.gov
|
| Organization name |
NIDDK
|
| Department |
GBB
|
| Street address |
5/205 Memorial Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE34785 |
Genome-wide assay of Vezf1 and RNA Polymerase II binding |
|
| Relations |
| SRA |
SRX117812 |
| BioSample |
SAMN00779046 |
