|
| Status |
Public on May 01, 2019 |
| Title |
SMB56-DMSO-1 |
| Sample type |
SRA |
| |
|
| Source name |
medulloblastoma
|
| Organism |
Mus musculus |
| Characteristics |
cell line: SMB56
cell type: spontaneous medulloblastoma cells from Ptch+/ mice
passages: 10-15
genotype: Ptch+/-
treatment: Treated with DMSO for 8hr
|
| Treatment protocol |
SMB56 cells were treated with DMSO, 0.1 uM THZ1 or 1 uM GDC-0449 for 8 hours, SMB56-shSufu cells were treated with DMSO or 0.1 uM THZ1 for 8 hours
|
| Growth protocol |
SMB56 and SMB56-shSufu cell lines were cultured (typically 1 × 10E6 cells into a well of 6-well plate) as neurospheres in DMEM/F12 media (Gibco, 11330-032) containing 1×B27(-A) (Gibco, 12587-010) and 1×Antibiotic-Antimycotic (Gibco, 15240-062).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested in Trizol and extracted by using mirVana miRNA isolation kit.
RNA libraries were prepared for sequencing by service provider using standard Illumina protocols with Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The RNAseq reads were mapped to the hg19 reference genome using STAR (v2.5.3a)
FPKM was calculated using Cufflinks (v2.2.1)
Differential expression analysis was carried out using R package DESeq2 (v1.20.0)
|
| |
|
| Submission date |
Apr 30, 2019 |
| Last update date |
May 01, 2019 |
| Contact name |
Yujie Tang |
| E-mail(s) |
yujietang@shsmu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
280 South Chong-qing Rd
|
| City |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE130485 |
THZ1-induced transcriptional changes in SMO inhibitor responsive and resistant mouse hedgehog-driven medulloblastoma cells |
|
| Relations |
| BioSample |
SAMN11536797 |
| SRA |
SRX5770430 |
