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Sample GSM3333420 Query DataSets for GSM3333420
Status Public on Aug 16, 2018
Title T24-SOX4-Knockdown-rep3
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

Data table header descriptions
ID_REF
VALUE RMA normalized

Data table
ID_REF VALUE
TC0100006432.hg.1 3.688415
TC0100006433.hg.1 3.627273
TC0100006434.hg.1 4.165165
TC0100006435.hg.1 3.651886
TC0100006436.hg.1 4.125834
TC0100006437.hg.1 3.701666
TC0100006438.hg.1 7.979403
TC0100006439.hg.1 5.90767
TC0100006440.hg.1 3.333055
TC0100006441.hg.1 5.673975
TC0100006442.hg.1 3.710405
TC0100006443.hg.1 4.322591
TC0100006444.hg.1 3.604519
TC0100006445.hg.1 3.297805
TC0100006446.hg.1 3.912028
TC0100006447.hg.1 16.03731
TC0100006448.hg.1 3.946136
TC0100006449.hg.1 4.142681
TC0100006450.hg.1 4.018616
TC0100006451.hg.1 4.414554

Total number of rows: 138745

Table truncated, full table size 3668 Kbytes.




Supplementary file Size Download File type/resource
GSM3333420_LBI11799-0013_T24-Prox_1-7_1-16_5-6_.CEL.gz 29.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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