|
| Status |
Public on Jan 23, 2022 |
| Title |
H2.35 cell treated with GSK8573 - H3K27ac rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H2.35 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: H2.35 cells
cell type: hepatocytes
treatment: control
chip antibody: anti-H3K27ac (Abcam #4729)
|
| Treatment protocol |
Cell were treated with 500 nM of GSK8573 or GSK2801 for 3 days before collection
|
| Growth protocol |
H2.35 (ATCC, source: BALB/c female mouse) immortalized hepatocytes were cultured in DMEM (Life Technologies) supplemented with 4% (vol/vol) FBS, 1× Pen/Strep solution (Thermo Scientific HyClone) and 200nM Dexamethasone (Sigma). Cells were cultured at 37°C and 5% CO2 in a humidified incubator.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 37% formaldehyde for 5 minutes at RT with shaking, followed by glycine to a final concentration of 125 mM for 5 minutes to stop fixation. Cell were sonicated with a probe sonicator to produce 250-500 bp long DNA fragment. Sonicated lysates were incubated with corresponding antibodies overnight at 4C: anti-H3K27ac (Abcam #4729); anti-H3K4me3 (Abcam #8580); anti-H3K4me1 (Abcam #8895) and anti-Flag (Sigma F1804), followed by incubation of ChIP-grade Pierce™ magnetic protein A/G beads (Thermo Scientific) for 3 hours at 4C. DNA was purified with QIAquick PCR purification kit (Qiagen).
Library were constructed with NEBNext Ultra DNA Library Prep Kit (NEB)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were mapped to the mouse reference genome GRCm38 (mm10) using BWA aligner (version 0.7.5) with default parameters
Peak calling was performed using MACS (version 1.4.2) with options -c --nomodel --p 1e-5.
BigWig files were generated usning bamCoverage command from deeptools (version 3.5.0) with --smoothLength 50 --binSize 5 and --scaleFactor. The scaleFactors were normalization factors calculated from DiffBind based on the number of reads in peaks.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: BigWig files
|
| |
|
| Submission date |
Sep 06, 2021 |
| Last update date |
Jan 25, 2022 |
| Contact name |
Hao Zhu |
| E-mail(s) |
yuemeng.jia@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Cetern
|
| Street address |
6000 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75202 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE183500 |
In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration [H2-ChIP-seq] |
| GSE183502 |
In vivo CRISPR screening reveals druggable regulators of mammalian tissue regeneration |
|
| Relations |
| BioSample |
SAMN21242838 |
| SRA |
SRX12023006 |
