|
| Status |
Public on Nov 07, 2022 |
| Title |
shScramble_Condition_A_4 |
| Sample type |
SRA |
| |
|
| Source name |
Bovine superficial zone articular chondrocytes
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Articular cartilage
cell type: Chondrocytes
shRNA treatment: Scramble shRNA
tgf treatment: TGFalpha
|
| Treatment protocol |
Ultracentrifuge-concentrated shScramble or shCreb5 lentivirus was added into DMEM/F12 medium (with 10% FBS) containing 7.5 μg/ml DEAE-Dextran (to increase infection efficiency). Twenty-four hours after infection, medium was replaced with new DMEM/F12 medium (with 10% FBS) containing 0.8 μg/ml puromycin for selection. After puromycin selection for 5 days, shScramble or shCreb5 infected superficial zone articular chondrocytes were replated onto low attachment tissue culture plates (Corning #3471 or #3473) in DMEM/F12 medium (with 10% FBS) for forty-eight hours in either the presence of TGF-α (100 ng/ml) alone (condition A) or in the presence of both TGF-α (100 ng/ml) and TGF-β2 (20 ng/ml) (condition AB).
|
| Growth protocol |
Newly isolated bovine superficial zone articular chondrocytes were cultured (in DMEM/F12 plus 10% FBS) for two days before infection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Trizol agents (Life Technologies)
KAPA mRNA HyperPrep Kits (Roche)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The RNA-Seq data were processed using the bcbio-nextgen pipeline.
Raw counts were obtained using Salmon.
Genome_build: Bovine genome UMD3.1 (release 94)
Supplementary_files_format_and_content: CSV, raw counts for each gene
|
| |
|
| Submission date |
Aug 11, 2021 |
| Last update date |
Nov 07, 2022 |
| Contact name |
Zhu Zhuo |
| E-mail(s) |
zzhuo@hsph.harvard.edu
|
| Organization name |
Harvard TH Chan School of Public Health
|
| Department |
Department of Biostatistics
|
| Lab |
Harvard Bioinformatics Core
|
| Street address |
401 Park Dr
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02130 |
| Country |
USA |
| |
|
| Platform ID |
GPL23055 |
| Series (1) |
| GSE181883 |
Creb5 coordinates synovial joint formation with the genesis of articular cartilage |
|
| Relations |
| BioSample |
SAMN20710010 |
| SRA |
SRX11717016 |
