|
| Status |
Public on Mar 11, 2021 |
| Title |
NRVCs treated with PE_ssRNA_seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Neonatal rat ventricular cardiomyocytes
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: cardiac ventricle
age: post natal day 2
treatment: treated with PE for 24 hours
|
| Treatment protocol |
NRVCs treated with PE (20uM)) for 24h
|
| Growth protocol |
NRVCs were isolated by enzymatic disassociation repeatedly. All isolated cells were plated for 1 hours to remove non-cardiomyocytes. Non-adherent cells were then plated on 0.5% gelatin-coated plates and cultured in DMEM high glucose medium (Gibco) supplemented with sodium pyruvate(1X), GlutaMAX(1X) and 10% fetal bovine serum with antibiotics.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell total RNA was isolated using Trizol reagent.
Ribosomal RNA was depleted from the samples using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) protocol (NEB, #E6310). Purified RNA was directly processed with the NEBNext ® Ultra ™ II Directional RNA Library Prep Kit for Illumina (NEB, #7760) and converted into libraries.
strand-specific RNA-seq
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
For strand-specific RNA-seq , adaptor sequences were trimmed from raw RNA-seq data using cutadapt (v2.0.dev0).
Fragments were aligned to the rat genome (Rattus_norvegicus.Rnor_6.0) using STAR (v2.4.2a) with ENCODE standard options for long RNA-seq pipeline and the Ensembl transcriptome (Rattus_norvegicus.Rnor_6.0.94) as a reference.
We generated read counts using featureCounts (v1.6.4) with default options
Genome_build: Rattus_norvegicus.Rnor_6.0
|
| |
|
| Submission date |
Aug 08, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Youchen Yan |
| E-mail(s) |
yanych8@mail2.sysu.edu.cn
|
| Organization name |
The First Affiliated Hospital, Sun Yat-sen University
|
| Street address |
No.58 Zhongshan Road II
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL24688 |
| Series (2) |
| GSE155913 |
The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes [ssRNA-seq] |
| GSE155914 |
The translational landscape of phenylephrine-treated neonatal rat cardiomyocytes |
|
| Relations |
| BioSample |
SAMN15768111 |
| SRA |
SRX8911998 |
