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Sample GSM3568916 Query DataSets for GSM3568916
Status Public on Jan 19, 2019
Title OA model_Non surgery rep2
Sample type SRA
Source name knee joints
Organism Mus musculus
Characteristics disease state: OA mouse model
tissue: knee joints
treatment: Non surgery
Treatment protocol An OA mouse model was generated as previously described. Briefly, anterior cruciate ligament transection (ACLT) was performed on male C57BL/6 mice aged 8 weeks. For the ACLT surgery, after opening the joint capsule, the ACL was transected with microscissors under a surgical micro-scope. One week after surgery, lentiviruses expressing Luc, CBX were injected into the articular cavity. Eight weeks after lentivirus injection, the mice were euthanized and the joints were collected for RNA extraction. The RNA samples of one treatment group were mixed and three technical repeats were performed for RNA-seq.
Extracted molecule total RNA
Extraction protocol Total cellular RNA was extracted using TRIzol (Thermo Fisher Scientific) and genomic DNA was removed using a DNA-free kit (Thermo Fisher Scientific). Quality control and sequencing was done by Novogene Bioinformatics Technology Co.Ltd.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description Non surgery
Data processing Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to mm10 genome using hisat2 software.
Reads were counted by Htseq-count.
Differentially expressed genes were calculated by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is HTseq reads count.
Submission date Jan 18, 2019
Last update date Jan 20, 2019
Contact name Zunpeng Liu
Phone +86 15510715055
Organization name State Key Laboratory of Stem Cell and Reproductive Biology
Department Institute of Zoology, Chinese Academy of Sciences
Lab Jing Qu
Street address Beichen West Road
City Beijing
ZIP/Postal code 100101
Country China
Platform ID GPL21273
Series (1)
GSE125320 Maintenance of nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis
BioSample SAMN10769685
SRA SRX5261278

Supplementary file Size Download File type/resource
GSM3568916_No_surgery_2.count.tsv.gz 189.3 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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