|
| Status |
Public on Aug 11, 2020 |
| Title |
mRNA_12_TNF_b |
| Sample type |
SRA |
| |
|
| Source name |
tissue-engineered cartilage
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tissue-engineered cartilage
time point (hr): 12
treatment: 20 ng/mL TNF-alpha
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen tissue-engineered cartilage samples were homogenized with a miniature bead beater. Total cellular RNA was isolated using the mirVana miRNA Isolation Kit (Invitrogen) for small RNA sequencing or Total RNA Purification Plus Kit (Norgen) for mRNA sequencing.
miRNA: Illumina TreSeq Small RNA kit; mRNA: Illumina Ribo-Zero Gold kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq reads were trimmed with Trimmomatic and Cutadapt
reads were aligned with STAR aligner
reads were counted using featureCounts
Genome_build: mRNA-seq: mm10 from Gencode vM15; miRNA-seq: a custom murine miRNA database based on miRBase v22
Supplementary_files_format_and_content: tab-delimited text files contain non-normalized counts for each sample at each time point and condition
|
| |
|
| Submission date |
Mar 31, 2020 |
| Last update date |
Aug 11, 2020 |
| Contact name |
Alison Ross |
| Organization name |
Washington University in St. Louis
|
| Street address |
Couch Biomedical Research Building
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE147833 |
The miRNA-mRNA Interactome of murine iPSC-derived Chondrocytes in Response to Inflammatory Cytokines |
|
| Relations |
| BioSample |
SAMN14501990 |
| SRA |
SRX8036843 |
