|
| Status |
Public on Sep 28, 2023 |
| Title |
H3K27ac ChIP-seq in propionate-treated NRVMs |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal rat ventricular myocytes (NRVMs)
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Neonatal rat ventricular myocytes (NRVMs)
treatment: Serum-starved cells were incubated in 6mM sodium propionate for 48 h
chip antibody: H3K27ac
|
| Growth protocol |
Primary neonatal rat ventricular myocytes were isolated from P1/P2 hearts of 1-2 day old Sprague-Dawley rats by enzymatic digestion, and a ‘pre-plating’ step was introduced to reduce fibroblasts in the myocyte-containing supernatant. Cells were plated onto fibronectin-coated TC culture dishes and cultured in M2 medium (80% DMEM medium containing 24 mM NaHCO3 and 20% M199 medium with 26mM NaHCO3) and incubated in a 5% CO2 atmosphere. Initially, medium was supplemented with 10% horse serum, 5% newborn calf serum and penicillin/streptomycin mixture. Next day, cells were serum-starved, followed by incubation in either 3.05 mM (pH 6.4) or 24.4 mM (pH 7.4) NaHCO3 with addition of 0.05% DMSO, or 24.4mM NaHCO3 plus 3µM A485 (p300 inhibitor) for 48 h.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS and fixed in 1% FA for 10 minutes. Cells were sonicated to give fragments of 200-300bp, then pooled with fixed, sonicated Drosophila S2 cells at a ratio of 4:1 rat:Drosophila, followed by IP.
DNA libraries were made using the NEBnext Ultra II DNA library preparation kit for Illumina (Cat no. E7645).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trim_galore (to remove sequencing adaptors)
Alignment to the genome (Bowtie2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads using Picard
Reference normalization by scaling read counts to mapped Drosophila reads (dm6) in IP and input samples
Assembly: rn6
Normalized bigWig generation using Homer v4.11
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Sep 28, 2023 |
| Contact name |
Pawel Swietach |
| Organization name |
University of Oxford
|
| Department |
Department of Physiology, Anatomy & Genetics
|
| Street address |
Sherrington Building, Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3PT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE205837 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation [ChIP-Seq 2] |
| GSE205838 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation |
|
| Relations |
| BioSample |
SAMN28963032 |
| SRA |
SRX15667270 |
