|
| Status |
Public on Sep 28, 2023 |
| Title |
RNA_NRVM-BUT_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
polyA RNA-seq in control NRVMs treated with 6mM butyrate for 48h
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Neonatal rat ventricular myocytes (NRVMs)
treatment: Serum-starved cells were incubated in 6mM sodium butyrate for 48 h
|
| Treatment protocol |
Serum-starved cells were incubated in 6mM sodium propionate or sodium butyrate for 48h as indicated
|
| 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, where appropriate, by treatment with sodium propionate or sodium butyrate, with NaCl added to balance osmolality between treatment media.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions and eluted into nuclease-free water.
PolyA RNA was purified using the NEBNext Poly(A) mRNA magnetic isolation module (E7490) and DNA libraries were prepared using the NEBNext Ultra II Directional RNA library preparation kit for Illumina (E7765).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq reads were aligned to the rn6 genome using STAR
Duplicate reads were removed using samtools rmdup
Read counts were determined using featureCounts (Subread package)
Differential gene expression analysis was conducted using DESeq2
Assembly: rn6
|
| |
|
| 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 |
GPL25947 |
| Series (2) |
| GSE205835 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation [RNA-Seq 2] |
| GSE205838 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation |
|
| Relations |
| BioSample |
SAMN28963045 |
| SRA |
SRX15667224 |
