|
| Status |
Public on Jul 02, 2020 |
| Title |
PEFs_CTCF-input |
| Sample type |
SRA |
| |
|
| Source name |
PEFs_CTCF-input
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Large White pigs
cell type: pig embryonic fibroblasts (PEFs)
chip antibody: none
|
| Growth protocol |
Porcine embryo fibroblast (PEF) were isolated from 35-day-old fetuses of Large White pigs, which was mechanically dissociated and digested in DMEM supplemented with 0.5 mg/mL collagenase IV for 2.5 h at 38 ℃. Isolated PFFs were cultured in the Dulbecco’s modified Eagle’s medium (DMEM, HyClone) supplemented with 15% fetal bovine serum (FBS, Gibco), 2 mM GlutaMAX (Gibco) and 1% nonessential amino acids (NEAA, Gibco) for 24 h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was conducted according to previously described protocols devoloped by Zhu et al.with few modifications. PMID: 30922236
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
PEF-input-CTCF_1.fastq.gz
|
| Data processing |
All ChIP-Seq reads were mapped using bowtie2
Peaks were called using the MACS2 callpeak command with a q value of 0.01. Narrow peaks were called for all libraries.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Jul 02, 2020 |
| Contact name |
Feifei Li |
| E-mail(s) |
[email protected]
|
| Phone |
15101052702
|
| Organization name |
Beijing Institute of Genomics
|
| Street address |
Chaoyang West Road, No.1
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (2) |
| GSE153451 |
The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq] |
| GSE153452 |
The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos |
|
| Relations |
| BioSample |
SAMN15398108 |
| SRA |
SRX8631144 |
