|
| Status |
Public on Jun 01, 2021 |
| Title |
Ace_6_5 |
| Sample type |
SRA |
| |
|
| Source name |
Primary neonatal cardiomyocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: Ace
timepoint: 6h
|
| Treatment protocol |
Cells were treated for either 6 or 24 hours with the specified drugs or control.
|
| Growth protocol |
Primary neonatal rat cardiomyocytes were isolated and cultured according to the protocol published in Ryall et al, 2014. Cell were manintained for ~36 hours in plating media before being serum starved overnight before treatment exposure.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were lysed with Trizol, mized with chloroform and spun in phase-lock gel tubes inside a cold room. The upper phase was decanted into new tubes and isopropanol and glycogen were added to the mixture which was incubated at -20C overnight. DNA was removed using the TURBO DNA-free kit (Invitrogen, #!M1907).
RNA was sent to GeneWiz (https://www.genewiz.com/en) for PolyA selection, library construction, and sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
raw_gene_counts.csv
differential_expression.xlsx
|
| Data processing |
Kallisto v 0.46.0 was used to pseudo-align raw fastq files under default settings to the Rattus norvegicus Ensembl v96 transcriptome.
Transcript abundances were aggregated to the Entrez gene level using the tximport package in R.
Genes with low counts (<10) across all samples within a treatment group were removed.
Differentially expressed genes (DEGs) were determined using DESeq2 with a significance threshold of FDR < 0.1.
Genome_build: Ensembl v96 transcriptome
Supplementary_files_format_and_content: raw counts and differential expression for all genes
|
| |
|
| Submission date |
Feb 17, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Jason Papin |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Virginia
|
| Department |
Biomedical Engineering
|
| Lab |
Papin Lab
|
| Street address |
415 Lane Rd
|
| City |
Charlottesville |
| State/province |
VA |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE166957 |
Identifying metabolic adaptations of rat cardiomyocytes in response to cardiotoxicity |
|
| Relations |
| BioSample |
SAMN17956517 |
| SRA |
SRX10120557 |
