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Status |
Public on Sep 02, 2021 |
Title |
RNA-seq_BCAA_rep2 |
Sample type |
SRA |
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|
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
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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
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|
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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 |