|
| Status |
Public on Jul 28, 2014 |
| Title |
Input_TRIMKD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic Stem Cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: none
treatment: Trim28 siRNA
|
| Treatment protocol |
ES cells were transfected with siRNAs at 50 nM concentration with lipofectamine 2000
|
| Growth protocol |
ES cells were cultured in M10 medium as described in the manuscript
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ES cells were crosslinked with formaldehyde and lysed. Chromatin was sonicated, and ChIP was performed as described in the manuscript.
Libraries were constructed using the SPRI-TE Nucleic Acid Extractor (Beckman Coulter, Indianapolis, IN) with a size selection of 200-400bp
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Input_TRIMKD_coverage.bw
|
| Data processing |
Basecalls performed using standard Illumina pipeline
Reads with mean Phred quality <20 were filtered
Reads were aligned to mm9 assembly using bowtie 0.12.8 employing parameters -v2 -m1
Duplicates reads were removed using Picard tools 1.74
Reads were extended to mean fragment length (150 nt), replicates were merged, and read coverage tracks were generated using bedtools 2.16.2
Genome_build: mm9
Supplementary_files_format_and_content: bigWig, read coverage
|
| |
|
| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
David Fargo |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Environmental Health Sciences
|
| Department |
HHS
|
| Lab |
Integrative Bioinformatics
|
| Street address |
P.O.Box 12233
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE48253 |
TRIM28 regulates RNA polymerase II promoter proximal pausing and entry into processive elongation |
|
| Relations |
| BioSample |
SAMN02212585 |
| SRA |
SRX314736 |
