|
| Status |
Public on Jun 27, 2019 |
| Title |
Gm13157 |
| Sample type |
SRA |
| |
|
| Source name |
F9 EC cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: F9 EC cells
overexpression: Gm13157
chip antibody: FLAG (F1804)
tag: N-3XFLAG
ChIP: O'Geen et al. 2010
mapping: Bowtie (-5 3 --best)
peak calling parameters: p-value < 1e-10, enrichment > 20
input: F9_Input + FLAG_control
|
| Treatment protocol |
Cells were cross-linked in 1% formaldehyde for 10 minutes before ChIP.
|
| Growth protocol |
F9 EC cells were grown on gelatine coated plates in DMEM supplemented with 10% FBS, ES cells were grown in standard ES media with 20% FCS and LIF or in 2i media as indicated in the sample information.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was purified and immunoprecipitated according to previously described protocols as indicated in the sample information.
DNA SMART kit (Takara) or Truseq (Illumina)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped using Bowtie or Bowtie2, as indicated in the sample information.
Mapped reads were converted to Bigwig files (normalized voverage to 1x) with DeepTools (control ChIPs were substracted from ChIP samples).
Peaks were called using MACS (version 1.4.2) with parameters as indicated in the sample information over Input and/or ChIP control samples, as indicated. For further analysis, the 200 bp region around the peak summit was used.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files and MACS14 peaks of all KRAB-ZFPs (200 bp core regions around peak summit)
|
| |
|
| Submission date |
Jun 04, 2018 |
| Last update date |
Jun 15, 2020 |
| Contact name |
Gernot Wolf |
| Organization name |
NIH
|
| Department |
NICHD
|
| Lab |
Macfarlan lab
|
| Street address |
6 Center Drive
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE115287 |
Genome-wide binding patterns of murine KRAB zinc finger proteins |
| GSE115291 |
Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice |
|
| Relations |
| BioSample |
SAMN09322662 |
| SRA |
SRX4159296 |
