|
Status |
Public on Jan 22, 2021 |
Title |
CTL-3 |
Sample type |
SRA |
|
|
Source name |
primary rat chondrocytes
|
Organism |
Rattus norvegicus |
Characteristics |
strain background: Sprague Dawley cell type: primary rat chondrocytes genotype/variation: Transfection of adenovirus expressing vector control
|
Treatment protocol |
The cells were infected with replication-defective adenovirus encoding the complete Rip1 open reading frame (Ad-Rip1) or adenoviral vector (Ad-Ctl) at a multiplicity of infection (MOI) of 100 for 24 hrs.
|
Growth protocol |
The cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco) supplemented with 10% fetal bovine serum (FBS; HyClone) and antibiotics (penicillin G and streptomycin).
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction. Hiseq Sequencing Protocol
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
|
|
Data processing |
mRNA:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
miRNA
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to rat genome.
count counting
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: TXT file contain counts for each sample
|
|
|
Submission date |
Jan 21, 2021 |
Last update date |
Apr 08, 2021 |
Contact name |
cheng jin |
E-mail(s) |
houpengwei@novelbio.com
|
Organization name |
Peking University Third Hospital
|
Street address |
49 Huayuan Bei Lu
|
City |
beijing |
ZIP/Postal code |
100000 |
Country |
China |
|
|
Platform ID |
GPL24688 |
Series (1) |
GSE165219 |
RIP1 perturbation induces chondrocyte necroptosis and promotes osteoarthritis pathogenesis |
|
Relations |
BioSample |
SAMN17394080 |
SRA |
SRX9907255 |