|
| Status |
Public on Sep 01, 2018 |
| Title |
siUSP342 |
| Sample type |
SRA |
| |
|
| Source name |
MSCs+siUSP34
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell type: mesenchymal stem cells (MSCs)
genotype/variation: USP34 siRNA
|
| Treatment protocol |
Human MSCs were treated with USP34 or control siRNAs and cultured in osteogenic induction medium for 2 days prior to RNA isolation
|
| Growth protocol |
α-MEM (Gibco) supplemented with 10% fetal bovine serum (Gibco),100 units/ml penicillin (Gibco) and 100 μg/ml streptomycin (Gibco)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were harvested using an RNeasy mini kit (Qiagen).
Libraries were prepared using the Illumina TrueSeq mRNA sample preparation kit according to manufacturer’s instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
The reads were aligned to hg19 genome using Tophat.
Analysis of RNA-seq data was done using Cufflinks with Refseq mRNAs to guide assembly and the cummeRbund package in R
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance measurements,
|
| |
|
| Submission date |
Jun 14, 2018 |
| Last update date |
Sep 01, 2018 |
| Contact name |
Quan Yuan |
| E-mail(s) |
yuanquan@scu.edu.cn
|
| Organization name |
West China Hospital of Stomatology, Sichuan University
|
| Lab |
State Key laboratory of Oral Diseases
|
| Street address |
14 Third section, Renmin Nan Road
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE115789 |
Ubiquitin-specific protease USP34 controls osteogenic differentiation and bone formation by regulating BMP2 signaling |
|
| Relations |
| BioSample |
SAMN09425587 |
| SRA |
SRX4214130 |
