|
| Status |
Public on Apr 15, 2024 |
| Title |
Cardiomyocytes, DMSO22h, C3 |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Cavia porcellus |
| Characteristics |
tissue: Heart
cell line: Cardiomyocytes
cell type: Ventricular cardiomyocytes
genotype: Mature
treatment: DMSO
time point: 22H
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total R.N.A. extraction was conducted on isolated guinea pig ventricular cardiomy-ocytes exposed independently to 10 μM of DOX and to the vehicle control (DMSO) for 22 hours at room temperature. We used Trizol reagent to extract following the manufacturer's guidelines (Invitrogen). The extracted R.N.A. was resuspended in H2O DEPC (diethyl py-rocarbonate, Sigma–Aldrich) and quantified via spectrophotometry using the Nanodrop 2000 (Thermo Fisher Scientific).
A small R.N.A. library was constructed using the TruSeq Small R.N.A. Library Prep Kit (Illumina Inc., U.S.A.). . The quality control and the normalization of the readings obtained using the BaseSpace® App, Small RNA v1.0 (Illumina), the sequences converted into FastQ files, and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC (https://usegalaxy.org/).
TruSeq Small R.N.A. Library to miRNAs was sequenced on an Illumina HiSeq2500 platform. Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Read quality assessment was performed using MultiQC and validated in Galaxy using FastQC. Alignments of reads ranging from 17 to 35 nucleotides in length were performed against the Homo sapiens reference genome.
Assembly: Homo sapiens maskedPAR (UCSC hg19)
Supplementary files format and content: Quality control and normalization of the resulting reads was performed using the BaseSpace® Small RNA v1.0 app (Illumina), with subsequent conversion of the sequences to FastQ files. and the quality of the readings was analyzed multiQC and confirmed in Galaxy by FastQC. The alignments for readings obtained between 17 and 35 nt against the reference genome for Homo sapiens.
|
| |
|
| Submission date |
Apr 15, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Yohana Dominguez |
| E-mail(s) |
lydominguezr@unal.edu.co
|
| Phone |
3012352029
|
| Organization name |
National Institute of Health
|
| Department |
Sub-Direction of Scientific and Technological Research
|
| Lab |
Molecular Physiology Group
|
| Street address |
El Dorado avenue 51-20
|
| City |
Bogota DC |
| State/province |
Bogota |
| ZIP/Postal code |
111321 |
| Country |
Colombia |
| |
|
| Platform ID |
GPL22346 |
| Series (1) |
| GSE263950 |
Effect of direct exposure to Doxorubicin on the expression profile of miRNAs in guinea pig ventricular cardiomyocytes |
|
| Relations |
| BioSample |
SAMN40971276 |
| SRA |
SRX24250506 |
