|
| Status |
Public on Aug 26, 2024 |
| Title |
As4.1 cells, H89, p300, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
cell line: As4.1
chip antibody: p300 (Abcam, #ab1494)
treatment: H89
|
| Treatment protocol |
Cells were treated with 10 μM H89 or equivalent volume DMSO at 0, 24, and 48 hours.
|
| Growth protocol |
The renin-expressing As4.1 cell line (ATCC, CRL-2193) was maintained in high glucose DMEM (supplemented with 10% fetal bovine serum (both from Thermo Fisher Scientific) at 37°C in a humidified incubator containing 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were then fixed according to manufacturer protocol.
Library construction and sequencing were performed by Active Motif (Carlsbad, CA) following manufacturer protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Raw sequencing reads were processed using the `nf-core/chipseq` pipeline (version 2.0.0) with alignment to the GRCm38/mm10 mouse genome. Enriched genomic regions for both H3K27ac and p300 were determined using MACS2 (Model-based analysis of ChIP-seq 2) with default settings by comparing ChIP to input samples. Differential binding analysis was then performed using the `DiffBind` R package. Differentially enriched regions were annotated using the `ChIPpeakAnno` and `clusterProfiler` R packages.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig - merged signal tracks, BED - consensus or enriched peaks (except input)
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
Aug 26, 2024 |
| Contact name |
Jason Paul Smith |
| E-mail(s) |
jasonsmith@virginia.edu
|
| Phone |
9193455043
|
| Organization name |
University of Virginia
|
| Department |
Pediatrics
|
| Lab |
Gomez Sequeira-Lopez
|
| Street address |
409 Lane Rd
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE254941 |
Renin Regulatory Pathway Inhibition Epigenetically Silences *Ren1* (ChIP-Seq) |
| GSE254945 |
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State |
|
| Relations |
| BioSample |
SAMN39749783 |
| SRA |
SRX23509733 |
