|
| Status |
Public on Jul 24, 2017 |
| Title |
ChIP-Seq analysis of PRDM15 in serum+lif Prdm15KO mES cells replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs cultured in SL
|
| Organism |
Mus musculus |
| Characteristics |
cell type: ESCs
passages: 30-40
strain: C57BL/6
chip antibody: PRDM15 antibody (in house)
|
| Treatment protocol |
OHT (50nM) 4 days before fixing the cell
|
| Growth protocol |
Serum+Lif
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated cells and histone-DNA complexes were isolated with antibody.
Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ES_Prdm15KO_rep2
|
| Data processing |
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the following configurations : -v 2 -m 1 -p 2 --best --strata --quiet –solexa1.3-quals
Peak calling was done by MACS 2.0.10 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated from the BAM alignment files, narrowpeak files were generated by MACS 2.0.10
|
| |
|
| Submission date |
Apr 24, 2017 |
| Last update date |
Apr 17, 2020 |
| Contact name |
Jingxian Zhang |
| E-mail(s) |
zhangjingxian.nus@gmail.com
|
| Organization name |
Institute of Molecular and Cell Biology (IMCB), A-Star, Singapore
|
| Department |
IMCB
|
| Street address |
61 Biopolis Drive Proteos
|
| City |
Singapore |
| State/province |
Singpaore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE73692 |
Genome-wide mapping of PRDM15 binding in pluripotent mouse Embryonic Stem Cells (mESCs) |
| GSE73694 |
PRDM15 safeguards naïve pluripotency by transcriptionally regulating WNT and MAPK/ERK signaling |
|
| Relations |
| BioSample |
SAMN06821045 |
| SRA |
SRX2754636 |
