|
| Status |
Public on Feb 01, 2024 |
| Title |
IP_RORĪ³_Vehicle_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Liver
strain: three-breed cross Duroc x (Landrace x Yorkshire)
chip antibody: anti-RORgamma rabbit serum was generated by Covance, using purified GST-human RORgamma fragment (amino acids 79-301) expressed in Escherichia coli.
agent: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Liver were collected and fresh frozen in liquid nitrogen.Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's paired-end DNA sample Prep kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Sequencing tags were mapped against the SUS Scrofa (Pig) reference genome (Sscrofa11.1) using Bowtie 2.
Uniquely mapped tags were used for peak calling by MACS(2.1.0) to identify regions of ChIP-Seq enrichment over background.
A q value threshold of enrichment of 5 x 10^-2 was used for all data sets. by using ngs.plot (https://github.com/shenlab-sinai/ngsplot)
Normalized genome-wide signal coverage tracks from raw read alignment files were built by MACS2, fold-enrichment normalized wiggle files were generated by MACS, UCSC tools (http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig/bedClip) and bedTools (http://code.google.com/p/bedtools/).
Visualization of ChIP-seq singnal at enriched genomic regions(avgprof and heatmap) was achieved
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: bigwig files were generated using MACS2 and UCSC tools
|
| |
|
| Submission date |
Feb 10, 2021 |
| Last update date |
Feb 01, 2024 |
| Contact name |
Demin Cai |
| E-mail(s) |
demincai@yzu.edu.cn
|
| Organization name |
Yangzhou University
|
| Street address |
Daxue South Road 88
|
| City |
Yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL9126 |
| Series (1) |
| GSE166520 |
ChIP-seq genome-wide maps of nuclear receptor RORĪ³ chromatin state in the liver of pig exposed to mycotoxin |
|
| Relations |
| BioSample |
SAMN17850080 |
| SRA |
SRX10064982 |
