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Status |
Public on May 01, 2024 |
Title |
Aging SNL CCs-1 |
Sample type |
SRA |
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Source name |
Primary articular chondrocytes
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Organism |
Mus musculus |
Characteristics |
cell type: Primary articular chondrocytes genotype: WT condition: aging SNL CCs
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
MGISEQ-2000RS |
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Description |
BA
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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.
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Submission date |
Apr 16, 2024 |
Last update date |
May 01, 2024 |
Contact name |
Dalin Chen |
E-mail(s) |
dalincc@smu.edu.cn
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Organization name |
Guangdong Institute of Orthopedics
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Street address |
295 Changxing Road
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City |
Guangzhou |
ZIP/Postal code |
510000 |
Country |
China |
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Platform ID |
GPL30215 |
Series (1) |
GSE264103 |
Aged skin exacerbates experimental osteoarthritis via enhanced IL-36R signaling |
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Relations |
BioSample |
SAMN40989075 |
SRA |
SRX24279621 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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