|
| Status |
Public on Jun 02, 2016 |
| Title |
NCCIT.PRDM14 |
| Sample type |
SRA |
| |
|
| Source name |
NCCIT cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCCIT Embryonal Carcinoma cell line
chip antibody: PRDM14 (Homemade)
|
| Growth protocol |
mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). NCCIT cells were grown in RPMI1640 with 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Reads were mapped to mm9 or hg19 with BOWTIE -m4 -v2
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: FP10M-normalized bigWigs
|
| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Danny Reinberg |
| E-mail(s) |
reinbd01@nyumc.org
|
| Phone |
212-263-9036
|
| Organization name |
NYU School of Medicine / HHMI
|
| Street address |
522 First Avenue, 2nd floor Rm 211
|
| City |
New York City |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE71675 |
A Co-repressor CBFA2T2 regulates pluripotency and germline development [ChIP-seq] |
| GSE71676 |
A Co-repressor CBFA2T2 regulates pluripotency and germline development |
|
| Relations |
| BioSample |
SAMN03952771 |
| SRA |
SRX1131599 |
