|
| Status |
Public on Sep 21, 2021 |
| Title |
input_SCNT_4cell |
| Sample type |
SRA |
| |
|
| Source name |
somatic cell nuclear transfer embryos
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: somatic cell nuclear transfer embryos
developmental stage: 4cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA extraction of 200 PFFs or 50 4-cell SCNT embryos are performed by using ULI-NChIP protocol as previously described (Brind'Amour et al., 2015).
Raw ChIP DNA material is used for library construction by KAPA HyperPrep Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava (v1.8.2) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads.
ChIP-seq reads were mapped to Sscrofa11.1 reference genome using Bowtie2 (v2.3.3.1).
Multiple mapped reads, PCR duplicates, and reads that have a map quality score less than 30 were removed.
Peak calling was performed by MACS2 (v2.2.5) with the parameters "macs2 callpeak –n Sample –g 2.2e9 -B -p 0.05" relative to input samples.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: bigwig files were generated using deeptools.
|
| |
|
| Submission date |
Nov 16, 2020 |
| Last update date |
Sep 23, 2021 |
| Contact name |
Jing-Jing Zhang |
| E-mail(s) |
jjzhang@webmail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Department |
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction
|
| Lab |
Miaolab
|
| Street address |
1 Lion Rock Street
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (2) |
| GSE161525 |
Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation [ChIP-Seq] |
| GSE161527 |
Resolving multiple epigenetic barriers to pig SCNT-mediated reprogramming during embryonic genome activation |
|
| Relations |
| BioSample |
SAMN16809123 |
| SRA |
SRX9514144 |
