|
| Status |
Public on Mar 15, 2022 |
| Title |
2Y_ATACseq_replicate_1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Bama pig
tissue: Liver
age: 2-years-old
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chopped frozen liver tissue was resuspended in homogenization buffer, and grounded under homogeneous solution, followed by filtered with a cell strainer. Cell pellets were obtained by centrifugation.
After iodixanol density gradient centrifugation, the nuclei band was collected form the resuspended sediment. Then 50,000 nuclei were resuspended in the Tn5 transposase reaction mix with two adapters. The transposition reaction was incubated at 37°C for 30 min. The fragmented DNA was purified and amplified with a limited PCR cycle using index primers. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
ATAC-seq datas was performed using trim-galore (version 0.6.4)
ATAC-seq read pairs were mapped using Bowtie2 (version 2.2.6)
Mitochondrial alignments, low-quality alignments (q<10) and PCR duplicates were removed using SAMtools (version 1.3.1)
ATAC peaks were called using MACS2
Genome_build: Susscrofa11.1
Supplementary_files_format_and_content: ATAC peak files
|
| |
|
| Submission date |
Dec 05, 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 |
SAMN23574776 |
| SRA |
SRX13294046 |
