|
| Status |
Public on Apr 09, 2023 |
| Title |
Intestine epithelium, drug stimulated rep2 |
| Sample type |
SRA |
| |
|
| Source name |
intestine epithelium
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: intestine epithelium
treatment: Stimulated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed with homogenization buffer for 10 minutes. After lysis, accesible chromatin frgments are separated using Tn5 transpotase and subsequent centrifugation.
Libraries were prepared using TruePrep DNA Library Prep Kit V2 for Illumina from Vazyme. 10ng of DNA was used for input and IP samples. Libraries were amplified using 13 cycles on thermocycler.Amplified libraries were size-selected at 200-300bp in length.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
2D-1
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim-galore v0.6.6, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the Ensembl Sus scrofa "Large White" genome(v1.105) using Bowtie2 (v2.4.2). Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the bamCoverage in deeptools package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: bigwig, narrowPeak
|
| |
|
| Submission date |
Apr 02, 2023 |
| Last update date |
Apr 11, 2023 |
| Contact name |
Jing Wang |
| E-mail(s) |
wangjing976119@126.com
|
| Organization name |
Beijing Academy of Agriculture and Forestry Sciences
|
| Department |
Institute of Animal Husbandry and Veterinary Medicine
|
| Street address |
Shuguanghuayuan middle road #9, Haidian district
|
| City |
Beijing |
| ZIP/Postal code |
100097 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE228772 |
Deoxyshikonin-induced chromatin accesibility changes in porcine intestinal epithelial cells |
|
| Relations |
| BioSample |
SAMN34042765 |
| SRA |
SRX19846034 |
