|
| Status |
Public on Oct 31, 2018 |
| Title |
TAZ-K treated cardiomyocytes rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Primary neonatal rat cardiomyocytes
strain: Wistar
|
| Treatment protocol |
Cardiomyocytes were starved (0.1% FCS) for 6 hours and subsequently treated with vehicle or TAZ-K (10 µM) for 24 hours.
|
| Growth protocol |
Primary neonatal rat cardiomyocytes were prepared from the ventricles of 1-day-old Wistar rats. The isolated and dispersed cardiac cells were incubated for 80 minutes to remove non-cardiomyocytes. The unattached viable cells, which were rich in cardiomyocytes, were cultured on gelatin-coated dishes at 37°C in DMEM media supplemented with 10% FCS for 24 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from cardiomyocytes was extracted using a RNeasy Mini Kit (Qiagen, Hilden, Germany) was used according to the manufacturer's protocol.
RNA sequencing libraries were generated with a TruSeq RNA Library Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacture's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were mapped to the rat genome (rn5) using Bowtie (version 1.1.1) with the parameters ‘-S -m 1 -l 36 -n 2 mm9’.
RPKM was calculated with reads mapped to the genome using DEGseq (version 1.8.0).
Genome_build: rn5
Supplementary_files_format_and_content: file includes RPKM values for each sample
|
| |
|
| Submission date |
Feb 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Seitaro Nomura |
| E-mail(s) |
senomura-cib@umin.ac.jp
|
| Phone |
81338155411
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Cardiovascular Medicine
|
| Street address |
7-3-1, Hongo, Bunkyo-ku
|
| City |
Tokyo |
| State/province |
Select a State or Province |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE95274 |
The effect of TAZ-K in neonatal rat cardiomyocytes |
|
| Relations |
| BioSample |
SAMN06434385 |
| SRA |
SRX2583775 |
