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| Status |
Public on Aug 26, 2024 |
| Title |
As4.1 cells treated with 1 μM JQ1, replicate 2 |
| Sample type |
SRA |
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| Source name |
kidney
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| Organism |
Mus musculus |
| Characteristics |
tissue: kidney
cell line: As4.1
treatment: JQ1
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| Treatment protocol |
At 0-, 24-, and 48-hours, cells were treated with either 10μM H89, 10μM A-485, 1μM JQ1, or equivalent volume DMSO.
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| 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.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
After 48 hours, 50,000 cells were collected, washed 3X with 5 mL dPBS (Dulbecco's Phosphate Buffered Saline, Gibco, UK), treated with Lysis Buffer, and resuspended.
Tagmentation was performed using a Nextera DNA library Prep Kit (Illumina) according to the manufacturer's directions.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
For initial processing of sequenced reads, the 150 bp paired-end reads were aligned to the mouse genome (GRCm38/mm10) using the PEPATAC (v0.10.4) pipeline. Enzymatic bias of aligned reads was corrected using `seqOutBias`.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig files represent the processed, bias-corrected ATAC-seq signals.
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| Submission date |
Feb 02, 2024 |
| Last update date |
Aug 26, 2024 |
| Contact name |
Jason Paul Smith |
| Organization name |
University of Virginia
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| Department |
Pediatrics
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| Lab |
Gomez Sequeira-Lopez
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| Street address |
409 Lane Rd
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| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22903 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE254940 |
Renin Regulatory Pathway Inhibition Epigenetically Silences *Ren1* (ATAC-Seq) |
| GSE254945 |
Inhibition of Renin Expression Is Regulated by an Epigenetic Switch From an Active to a Poised State |
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| Relations |
| BioSample |
SAMN39749619 |
| SRA |
SRX23509745 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8060487_JQ1_02.bigWig |
156.8 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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