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Sample GSM8060494 Query DataSets for GSM8060494
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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