|
| Status |
Public on Sep 21, 2023 |
| Title |
sows liver (low bile acid group) IP |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: liver
cell type: hepatocytes
Sex: female
chip-antibody: Anti-H4K12la (PTM1411)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One hundred million cells were fixed with 1% formaldehyde and sonicated for 8 min (10s on and 15s off) on ice with a 2-mm microtip with a 40% output control and 90% duty cycle setting.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| 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 Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. 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: http://ftp.ensembl.org/pub/release-104/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa.gz
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Sep 26, 2022 |
| Last update date |
Sep 21, 2023 |
| Contact name |
Tongxin Wang |
| E-mail(s) |
wangtongxin@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Hongshan Huazhong Agricultural University
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE214238 |
H4K12 Lactylation-activated c-JUN signaling aggravates bile acid dysfunction in intrahepatic cholestasis during pregnancy |
|
| Relations |
| BioSample |
SAMN31024317 |
| SRA |
SRX17712432 |
