|
| Status |
Public on Sep 02, 2021 |
| Title |
RNA-seq_BCAA_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Adipose-derived mesenchymal stem cells
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Adipose-derived mesenchymal stem cells
strain: Sprague Dawley
treatment: treated with 3.432mM BCAA for 12 hours in the presence of 100uM hydrogen peroxide
|
| Treatment protocol |
treated with vehicle or 3.432mM BCAA for 12 hours.
|
| Growth protocol |
customized BCAA-free DMEM/HG containing 10% FBS and 1% penicillin/streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using TRIzol reagent. A total of 3 μg of RNA per sample was utilized for RNA library preparation with the NEBNext® UltraTM RNA Library Prep Kit for Illumina® for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
(RNA-Seq) Trimmomatic software were used to remove adapter and low quality reads. [Bolger et al., Bioinformatics, 2014]
(RNA-Seq) Quality distribution plot and base content distribution were generated by FASTQC.
(RNA-Seq) STAR is used to align clean reads to reference genome. [Dibin et al., STAR: ultrafast universal RNA-seq aligner.Bioinformatics, 2013]
(RNA-Seq) Read counts for individual transcripts of each sample were produced with HTSeq-count. [Anders et al., HTSeq--a Python framework to work with high-throughput sequencing data, Bioinformatics, 2015]
Genome_build: rn6
Supplementary_files_format_and_content: raw counts
|
| |
|
| Submission date |
Aug 30, 2021 |
| Last update date |
Sep 02, 2021 |
| Contact name |
Fuyang Zhang |
| E-mail(s) |
plazhangfuyang@163.com, plazhangfuyang@aliyun.com
|
| Organization name |
Xijing hospital
|
| Department |
Cardiology
|
| Street address |
127 West Changle Rd
|
| City |
Xi'an |
| State/province |
Shaanxi |
| ZIP/Postal code |
710032 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE183025 |
Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury [RNA-Seq] |
| GSE183028 |
Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury |
|
| Relations |
| BioSample |
SAMN21037689 |
| SRA |
SRX11964794 |
