|
| Status |
Public on Aug 16, 2018 |
| Title |
T24-SOX4-Knockdown-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
T24 cell line stably expressing KRAB-dCas9-mcherry + SOX4 sgRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T24
cell line type: bladder cancer
|
| Treatment protocol |
No drug treatments were performed on cell lines
|
| Growth protocol |
T24 Bladder cancer cell lines were obtained from American Type Culture Collection. 5637 cells were maintained in DMEM growth media supplemented with 10% FBS, 1% L-Glutamine, and 1% Penicillin-Streptomycin. Cells were cultured in a 37C incubator with humidified atmosphere of 5% CO2. T24-scrambled-sgRNA and T24-SOX4-sgRNA were grown as previously stated with addition of 1.5ug/ml puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cultured cells using Qiagen RNAeasy kit as per manufacturer’s protocol. RNA concentrations were measured using NanoDrop Spectrophotometer (Mode # ND-1000). RNA samples were processed at the Emory Integrated Genomics Core Facility for quality control analysis and analyzed using the Affymetrix Clariom D Genechip platform.
|
| Label |
biotin
|
| Label protocol |
Lysates were placed in eppendorff tubes and manually labelled
|
| |
|
| Hybridization protocol |
Emory Integrated Genomics Core. Emory University, Atlanta, GA
|
| Scan protocol |
Emory Integrated Genomics Core. Emory University, Atlanta, GA
|
| Data processing |
Gene level signal was generated by RMA normalization. Differential gene expression was determined using the samr package in R Bioconductor with 500 permutations, minimum fold change of 1.5 fold, and median FDR < 0.05.
|
| |
|
| Submission date |
Aug 15, 2018 |
| Last update date |
Aug 16, 2018 |
| Contact name |
Josue Moran |
| Organization name |
Emory University
|
| Street address |
615 Michael Street
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30340 |
| Country |
USA |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE118572 |
Expression data for T24 bladder cancer cell line - scrambled, SOX4-KD and SOX4 overexpression |
|
