|
| Status |
Public on Feb 15, 2023 |
| Title |
3D4/21, untreated, H3K27ac, rep1 [H3K27ac_00h_r1] |
| Sample type |
SRA |
| |
|
| Source name |
3D4/21
|
| Organism |
Sus scrofa |
| Characteristics |
cell line: 3D4/21
genotype: Wild-type
antibody: Abcam, ab4729
treatment: none; untreated
|
| Treatment protocol |
GSK126 was added to RPMI 1640 medium to make its final concentration as 5 μmol/L. The same volume of DMSO was added for the untreated control group. The control group and GSK126 treated group are collected for subsequent experiments.
|
| Growth protocol |
Porcine 3D4/21 alveolar macrophages were cultured in 1640 medium with 10% fetal bovine serum and 1% penicillin-streptomycin (100×), incubated in a constant temperature incubator with 37 ℃, 5% CO2 and saturated humidity.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-Seq for porcine alveolar macrophage was performed following our previous study (Sun et al. 2021, PMID: 34320657).
Chromatin fragmentation was performed using Diagenode Bioruptor Plus Sonicator. The antibody for H3K27ac (Abcam, ab4729) is used. The amount of chromatin is 20 μg per reaction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Data processing |
Reads were trimmed with TrimGalore v0.6.4 and then aligned to the corresponding reference genome (Sscrofa11.1.108) using Bowtie v2.3.5 with default settings. PCR duplicates were removed using the rmdup function of samtools v1.13. After confirming the data reproducibility, reads from biological replicates were pooled together for further analysis. Peak calling was performed with MACS v2.2.6 with default settings.
Assembly: Sscrofa11
Supplementary files format and content: narrowPeak (except for Input sample)
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
Feb 15, 2023 |
| Contact name |
Z LL |
| E-mail(s) |
MZ120201482@stu.yzu.edu.cn
|
| Phone |
13283789136
|
| Organization name |
yangzhouaxue
|
| Street address |
shuangqiaojiedao
|
| City |
yangzhou |
| ZIP/Postal code |
225009 |
| Country |
China |
| |
|
| Platform ID |
GPL32965 |
| Series (2) |
| GSE221476 |
Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages [ChIP-seq] |
| GSE221479 |
Inhibition of EZH2 causes retrotransposon derepression and immune activation in porcine lung alveolar macrophages. |
|
| Relations |
| BioSample |
SAMN32340970 |
| SRA |
SRX18799745 |
