|
| Status |
Public on Apr 01, 2021 |
| Title |
Cardiomyocytes RA1 |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: cardiomyocytes derived from E18.5 hearts
strain: mixed genetic background
treatment: atRA (100nM)
|
| Treatment protocol |
Cells were grown to around 60-70% confluency and treated with 100nM of all trans retinoic acid (sigma) for 48 hours or dmso for controls.
|
| Growth protocol |
E18.5 mouse hearts were pooled, minced and trypsin digested for 3 intervals of 15 minutes. At each interval media was removed and reaction stopped with cold FBS and trypsin was replaced for non-digested material. Collected media was then pooled, pelleted and the resulting cell suspension was plated for 1 hour on uncoated plates to remove contaminating fibroblasts. Non-adherent cardiomyoctes were transferred to collagen coated 6-well plates and cells grown to desired confluency in DMEM media supplemented with 10% FBS, pen/strep and glutamine at 37°C in 10% CO2 humidified chambers. Experiment was repeated four times in total. One well used for control and one for treatment for each dissection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Trizol extraction.
Libraries were prepared on a Beckman Fxp Automation system, using the Illumina TruSeq stranded polyA chemistry kit. 500 ng sample was used as input for the library prep.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
sequences were aligned using Burrows-Wheeler Aligner (bwa) version 0.7.12-r104 using standard parameters
differential anaylsis of gene expression was calculated using DESeq2 program with Genomatix software
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 13, 2020 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Andreas Schedl |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Nice
|
| Department |
iBV
|
| Street address |
Parc Valrose
|
| City |
Nice |
| ZIP/Postal code |
06100 |
| Country |
France |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE161429 |
Genome wide sequencing analysis of primary cardiomyocytes treated with all-trans retinoic acid |
|
| Relations |
| BioSample |
SAMN16792633 |
| SRA |
SRX9504670 |
