|
| Status |
Public on Mar 04, 2024 |
| Title |
MAC, siNC_1 |
| Sample type |
SRA |
| |
|
| Source name |
Articular cartilage
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Articular cartilage
cell line: Primary culture
cell type: Chondrocyte
treatment: Control siRNA
genotype: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted 36 h after transfection using the TRI reagent (Molecular Research Center, Inc.).
RNA sequencing libraries were constructed by Macrogen using the TruSeq Stranded mRNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of sequence reads was performed using FastQC.
Sequence reads were trimmed to remove low-quality bases and adapters using Trimmomatic v0.39.
Trimmed sequence reads were mapped against the mouse reference genome (GRCm39) using the STAR aligner
Assembly: mm39
Supplementary files format and content: tab-delimited files including read counts for each sample
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Mar 04, 2024 |
| Contact name |
Jin-Hong Kim |
| E-mail(s) |
snumrl301@gmail.com
|
| Organization name |
Seoul National University
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE230800 |
Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage [RNA-seq] |
| GSE230801 |
Predisposal of Interferon Regulatory Factor 1 Deficiency to Accumulate DNA Damage and Promote Osteoarthritis Development in Cartilage |
|
| Relations |
| BioSample |
SAMN34412595 |
| SRA |
SRX20122826 |
