|
| Status |
Public on Jul 04, 2023 |
| Title |
Y79 cells, THZ1 50nM 12h, 2 |
| Sample type |
SRA |
| |
|
| Source name |
Y79
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Y79
cell type: Retinoblastoma
genotype: WT
treatment: 50 nM THZ1, 12h
|
| Growth protocol |
The Y-79 and WERI-Rb-1 cell lines were cultured in Roswell Park Memorial Institute medium containing 10% fetal bovine serum and 1% penicillin/streptomycin. Incubation of all cell lines was carried out at 37 °C in a humidified 5% CO2 environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Y79 and WERI-Rb-1 cells were cultured in six-well plates and treated with dimethyl sulfoxide (0.1%) or THZ1 (50 nM) for 12 hours.
The sequencing libraries were created according to the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500) manufacturer's guidance.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Y79T2
|
| Data processing |
The reads were aligned to GRCh38 (Genome Reference Consortium Human Build 38 Organism).
The expression levels were evaluated using Cufflinks software (Trapnell, Williams et al. 2010) as FPKM (fragments per kilobase of exon per million fragments mapped).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
|
| |
|
| Submission date |
Jun 29, 2023 |
| Last update date |
Jul 11, 2023 |
| Contact name |
Hanyue Xu |
| E-mail(s) |
xhydoris@gmail.com
|
| Organization name |
West China Hospital, Sichuan University
|
| Street address |
Guoxuexiang street
|
| City |
Chengdu |
| State/province |
Sichuan |
| ZIP/Postal code |
610041 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE236205 |
Effect of CDK7 inhibitor on MYCN-amplified retinoblastoma |
|
| Relations |
| BioSample |
SAMN36083403 |
| SRA |
SRX20830527 |
