|
| Status |
Public on Nov 19, 2013 |
| Title |
MGHU3 Cells_Control siRNA_Biological Replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
MGHU3 Cells_Control siRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MGHU3
cell type: malignant urothelial cells
genotype/variation: FGFR3 Y375C mutation
transfected with: 5ug Control siRNA
|
| Treatment protocol |
Cells were transfected using the Neon system (Life Technologies). Following the manufacturer’s procedure, 1x10^6 cells were suspended in 100µl suspension solution containing 5 µg siRNA (Dharmacon) or plasmid and pulsed under program 3 for cells
|
| Growth protocol |
MGHU3 cells were propagated at 37°C in RPMI 1640 (Hyclone; Thermo Scientific, Rockford, IL) supplemented with 10% FBS (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was processed as recommended by Affymetrix, Inc. Briefly, RNA was isolated using TRIzol (Life Technologies) and passed through RNeasy spin columns (Life Technologies) for further clean up.
|
| Label |
Biotin
|
| Label protocol |
The Ambion WT expression kit (Life Technologies) was used to prepare RNA samples for whole transcriptome microarray analysis per manufacturer's instructions
|
| |
|
| Hybridization protocol |
2 ug of the labeled, fragmented single-stranded cDNA was then hybridized to probe sets on a Human AffymetrixGeneChip 1.0ST array.
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3.
|
| Description |
SAMPLE 2
|
| Data processing |
Data were imported into Partek Genomics Suite Version 6.6 software with the following operations being done to prepare the data for statistical analysis: 1) RMA Background Correction, 2) Quantile Normalization, 3) Log base 2 transformation, and 4) Summary of Probe sets using mean value. Statistical analysis consisted of one-way ANOVA with a single categorical variable, and gene lists were generated for those genes with fold-change magnitude > 2 and p-value with a false discovery rate (FDR) <.05.
|
| |
|
| Submission date |
Nov 18, 2013 |
| Last update date |
Nov 19, 2013 |
| Contact name |
Leslie Thompson |
| E-mail(s) |
[email protected]
|
| Organization name |
University of California, Irvine
|
| Street address |
Biological Sciences III
|
| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE52452 |
Gene expression data from MGHU3 bladder cancer cells (FGFR3-Y375C) treated with TAK1 siRNA and/or PD173074 |
|
