|
| Status |
Public on Sep 15, 2022 |
| Title |
LiverA_Cattle_input |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Bos taurus |
| Characteristics |
tissue: liver
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
none provided by the submitter
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
We used Trim Galore v0.4.0 and FastQC v0.11.2 software to trim the raw reads and obtain sequence quality reports.
The clean reads were mapping to the corresponding reference genome of each species using BWA-MEM software v0.7.17 with the default parameters,uplicated alignment reads were removed using the Picard Tools v2.25.0 with the parameter “REMOVE_DUPLICATES = true”.
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.
narrow peaks using MACS2 v2.1.1 with options “-q 0.01”.
bigWig files were generated using deepTools v3.1.1 with the follow parameters “--normalizeUsing CPM”.
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Jun 22, 2022 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Siqian Chen |
| E-mail(s) |
siqianchen1994@gmail.com
|
| Phone |
15652765993
|
| Organization name |
China Agricultural University
|
| Department |
College of Animal Science and Technology
|
| Lab |
National Engineering Laboratory for Animal Breeding
|
| Street address |
2rd, Yuanmingyuan West Road
|
| City |
Beijing |
| ZIP/Postal code |
100193 |
| Country |
China |
| |
|
| Platform ID |
GPL19172 |
| Series (1) |
| GSE206736 |
Dynamics of regulatory elements in the liver during ruminant evolution |
|
| Relations |
| BioSample |
SAMN29252822 |
| SRA |
SRX15831518 |
