|
| Status |
Public on Mar 15, 2022 |
| Title |
0d_H3K27ac_replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Bama pig
tissue: Liver
condition: Developmental stage
age: the birth day
Sex: female
chip antibody: H3K27ac (ab4729, Abcam)
|
| Treatment protocol |
Six two-years-old female pigs were fed with a high fat diet (15.12 MJ·kg-1 metabolizable energy, 11.26% crude protein, 6.8% fat and 5% lysine) for 22 weeks, compared with the pigs of two-years-old fed with well-characterized normal diet for 22 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were washed with PBS and incubated in lysis buffer. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). The histone-DNA complexes were isolated with H3K27ac and H3K4me3.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the Illumina TruSeq ChIP Sample Prep Set A and sequenced on Illumina HiSeq X Ten with PE150 method
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
0d_1
|
| Data processing |
Reads were mapped to the pig genome (Sscrofa 11.1) by BWA (v 0.7.15).
Samtools (v 1.3.1) was used to remove potential PCR duplicates.
Peaks were identified with MACS2 algorithms.
Super-enhancers were defined using the standard ROSE algorithms.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: Peaks file, text file
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Jing Li |
| E-mail(s) |
lijing-jane@foxmail.com
|
| Phone |
+8615882474902
|
| Organization name |
Sichuan Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Street address |
No. 211 Huimin Road, Wenjiang District
|
| City |
Chengdu |
| State/province |
China |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
|
| Platform ID |
GPL22475 |
| Series (1) |
| GSE176387 |
Three-dimensional geome study of procine livers during development and metabolic adaptation |
|
| Relations |
| BioSample |
SAMN18317840 |
| SRA |
SRX10588926 |
