|
| Status |
Public on Feb 26, 2021 |
| Title |
Duroc_2W_1_Spleen_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Sus scrofa |
| Characteristics |
breed: Duroc
tissue: spleen
age: 2 weeks
chip antibody: H3K4me3 (Millipore-04-745)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The frozen issues were ground to a fine powder with liquid nitrogen and fixed with 1% formaldehyde at room temperature for 20 min. Nuclear lysates were fragmented by Covaris S220 (Adaptive Focused Acoustics®). For each tissue, 300 μg of chromatin and 3 μg of H3K4me3 (Millipore-04-745) and H3K27ac (Abcam, ab4729) antibodies were used for ChIP-seq analysis.
ChIP–Seq libraries were constructed following Illumina protocols with minor modifications (Illumina, San Diego, CA), and sequenced on an illumina Hiseq X ten PE150 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
individual 1
|
| Data processing |
The clean data was obtained after removing reads with adapter contamination or low quality.
ChIP reads and Input reads were aligned to susScr11.1 genome with BWA v0.7.15.
Low MAPQ reads (less than 25) and duplicated reads of mapped bam files were removed with SAMTools v1.2 and Picard v1.126. Then the filtered bam file of each sample were used to call peak.
The narrow peaks and the bedgraph files of -log10(p-value) signal tracks for each replicate were generated with MACS2 v2.1.0 (-g genome.size -p 0.01 --nomodel --shift 0 --extsize n --keep-dup 1 -B --SPMR). The “n” for –extsize parameter were automatically calculated by the ENCODE ChIP-seq pipeline which was downloaded from GitHub website (https://github.com/kundajelab/chipseq_pipeline).
The narrow peaks were filtered with the cutoff for P<1E-05. The bigwig files of signal tracks were generated with MACS2 v2.1.0 and bedGraphToBigWig command based on bedgraph files from the last step.
Genome_build: susScr11.1
Supplementary_files_format_and_content: Bigwig files of signal tracks and bed files of narrow peaks for each sample.
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Feb 27, 2021 |
| Contact name |
Shuhong Zhao |
| E-mail(s) |
shzhao@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
No.1,Shizishan Street, Hongshan District
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE143288 |
A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome |
|
| Relations |
| SRA |
SRX7438644 |
| BioSample |
SAMN13676547 |
