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Status |
Public on Aug 26, 2024 |
Title |
As4.1 cells, H89, p300, rep1 |
Sample type |
SRA |
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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.
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|
|
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)
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|
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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 |