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Sample GSM8210471 Query DataSets for GSM8210471
Status Public on May 01, 2024
Title Aging SNL CCs-1
Sample type SRA
 
Source name Primary articular chondrocytes
Organism Mus musculus
Characteristics cell type: Primary articular chondrocytes
genotype: WT
condition: aging SNL CCs
Extracted molecule total RNA
Extraction protocol Lyse the cells using Trizol, centrifuge and transfer the supernatant into an EP tube containing chloroform/isoamyl alcohol (24:1) and mix well. After centrifugation, transfer the supernatant into a new EP tube containing isopropyl alcohol and mix well, then let it stand for 2 hours at (-20°C). After washing, wash 3 times with 75% ethanol. Finally, discard the supernatant and absorb the remaining liquid. After drying, add 20-200 μL DEPC water to dissolve the precipitate.
After quality inspection of the RNA, the secondary structure is opened through denaturation, and oligo(dT) magnetic beads are used to enrich the mRNA. Then a fragmentation reagent is added to fragment the mRNA, a reaction system is prepared, and the reaction program is set to synthesize one-strand and two-strand cDNA. Repair the double-stranded cDNA end, add an A base to the 3' end, and connect the adapter to the cDNA. PCR amplification is then performed, and uncirculated linear DNA molecules are digested. The single-stranded circular DNA molecule is then replicated through rolling circles to form a DNA nanoball (DNB) containing multiple copies. The obtained DNBs are added to the mesh holes on the chip using high-density DNA nanochip technology, and sequenced through combined probe anchored polymerization technology (cPAS).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model MGISEQ-2000RS
 
Description BA
Data processing The raw data obtained from sequencing was filtered using SOAPnuke (v1.5.6) to obtain clean data. Follow-up use of Dr. Tom's Multi-Omics Data Mining System (https://biosys.bgi.com) is used for data analysis, mapping and mining.
HISTA2 (v2.1.0)[2] software was used to align the clean data to the reference genome. Then, Ericscript (v0.5.5) was used for gene fusion detection and rMATS (v3.2.5) was used for alternative splicing and differential alternative splicing detection.
Align the clean data to the reference gene set using Bowtie2 (v2.3.4.3). Gene expression quantification was performed using RSEM (v1.3.1) software, and clustering heat maps of gene expression in different samples were plotted using pheatmap (v1.0.8).
Differential gene detection was performed using DESeq2 (v1.4.5) under conditions of Q value≤0.05 or FDR≤0.001.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of differential genes were performed using Phyper, and Qvalue≤0.05 was used as the threshold, which was defined as significant enrichment in candidate genes.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: This project uses SOAPnuke, a filtering software independently developed by Shenzhen BGI, for filtering. The filtered "Clean Reads" are saved in FASTQ format.
 
Submission date Apr 16, 2024
Last update date May 01, 2024
Contact name Dalin Chen
E-mail(s) dalincc@smu.edu.cn
Organization name Guangdong Institute of Orthopedics
Street address 295 Changxing Road
City Guangzhou
ZIP/Postal code 510000
Country China
 
Platform ID GPL30215
Series (1)
GSE264103 Aged skin exacerbates experimental osteoarthritis via enhanced IL-36R signaling
Relations
BioSample SAMN40989075
SRA SRX24279621

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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