|
| Status |
Public on Jun 24, 2021 |
| Title |
T24_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
bladder cancer cell line T24
|
| Organism |
Homo sapiens |
| Characteristics |
inhibitor: Negative control
cell line: T24
|
| Treatment protocol |
OICR-9429 was diluted at a stocking solution of 50mM in dimethyl sulfoxide (DMSO, Sigma), and cells were treated for 48h with 140µM of OICR-9429.
|
| Growth protocol |
T24 was cultured in RPMI-1640 (Gibco) and UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base-calling:bcl2fastq2 v2.19.1
Data filtering :in house
Read alignment:hisat2 v2.1.0
transcript assemble:htseq-count v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: excel files include normalize values for each Sample
|
| |
|
| Submission date |
Feb 12, 2020 |
| Last update date |
Jun 24, 2021 |
| Contact name |
Xu Chen |
| E-mail(s) |
[email protected]
|
| Organization name |
Sun Yat-sen Memorial Hospital
|
| Department |
Department of Urology
|
| Street address |
107. W. Yanjiang Road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE145158 |
Altered expression of genes in WDR5 inhibited (by OICR-9429) bladder cancer cells |
|
| Relations |
| BioSample |
SAMN14088127 |
| SRA |
SRX7712976 |
