|
Status |
Public on Nov 07, 2022 |
Title |
shCreb5_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: Creb5 3#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 |
SAMN20710012 |
SRA |
SRX11717018 |