|
| Status |
Public on Nov 16, 2023 |
| Title |
SCNT2 |
| Sample type |
SRA |
| |
|
| Source name |
somatic cell nuclear transfer embryos
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: embryo
development stage: 10 h after activation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After removing the zona pellucida, oocytes or embryonic cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al and Jingyi Wu et al. with slightly modification
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
clone-50-2
|
| Data processing |
Raw data was stored in FASTQ format, including the base sequence and corresponding quality information. Trimmomatic (v0.36) was used to remove adaptor-polluted or low-quality bases, and reads too short ( < 36 nt) were filtered out to get the clean data.
Clean data was mapped to reference genome by Bowtie2, and visualized by IGV
Peaks corresponding to the open region in genome were detected by MACS2
significantly different peaks between samples were acquired using Manorm
he enrichment analysis of GO term (http://geneontology.org/) or KEGG pathway (http://www.kegg.jp/) was based on hypergeometric test with the threshold q < 0.05, to find the significant enrichment of detected genes
Genome_build: Sus_scrofa.Sscrofa11.1.90.chr
Supplementary_files_format_and_content: bw
|
| |
|
| Submission date |
Nov 16, 2020 |
| Last update date |
Nov 16, 2023 |
| Contact name |
Xue Zhang |
| E-mail(s) |
2017205006@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
1 Weigang
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE161563 |
Identification of chromatin accessibility during the early stage of pig SCNT embryo reprogramming by ATAC-seq |
|
| Relations |
| BioSample |
SAMN16810810 |
| SRA |
SRX9515609 |
