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Sample GSM5028445 Query DataSets for GSM5028445
Status Public on Jan 22, 2021
Title CTL-1
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 SAMN17394082
SRA SRX9907253

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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