|
| Status |
Public on Jan 31, 2024 |
| Title |
CTN_50μM_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H9c2(2-1)
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: H9c2(2-1)
cell type: cardiomyoblast
treatment: CTN 50 μM
time: 48 h
|
| Treatment protocol |
Rat cardiomyoblast H9c2 cells were treated with 0 and 50 μM of CTN for 48 h in DMEM medium containing 10% FBS.
|
| Growth protocol |
Rat cardiomyoblast H9c2 cells were maintained in DMEM medium containing 10% FBS and subcultured for every 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed with TRIzol reagent according to manufacturer’s instruction (Invitrogen, Waltham, MA). RNA quality assessment was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturer’s protocol.
cDNA library construction was performed by Azenta Life Sciences, Inc. (Chelmsford, MA) according to manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads quality checked by fastqc
Raw reads trimmed by cutadapt
Trimmed raw reads aligned to rat reference genome by star
Alignment quality checked by rseqc
Read counts of gene normalized to CPM by edgeR
Assembly: Rattus norvegicus assembly mRatBN7.2 release 109
Supplementary files format and content: Tab-delimited TXT file containing read counts of each gene for each sample
Supplementary files format and content: CSV file containing log2CPM values of each gene for all the samples
|
| |
|
| Submission date |
Jun 02, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Jui-Feng Tsai |
| E-mail(s) |
f07447011@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Graduate Institute of Toxicology
|
| Street address |
No. 1, Sec. 1, Ren'Ai Rd,
|
| City |
Taipei |
| ZIP/Postal code |
100233 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE234049 |
Cardiotoxic effects of mycotoxin citrinin on mammalian cells revealed by transcriptome profiling |
|
| Relations |
| BioSample |
SAMN35573568 |
| SRA |
SRX20581091 |
