|
| Status |
Public on Mar 29, 2012 |
| Title |
Panc-1 Ctrl 1 |
| Sample type |
RNA |
| |
|
| Source name |
Panc-1_Control
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Panc-1
transfected with: pCIG (empty vector)
|
| Treatment protocol |
Cells were transfected with the control vector or Gli3T expressing vector using Lipofectamine 2000 reagent.
|
| Growth protocol |
Cells were cultutured in DMEM with 10% Fetal Bovine Serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from FACS sorted cells using Qiagen RNAeasy kit according to manufacturer protocol
|
| Label |
Biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials. Cocktails were heated at 99° for 5 minutes, then 45° for 5 minutes, and centrifuge at max speed for 1 minute. 200μl of hyb solution transfered to each array. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
SAMPLE 1
|
| Data processing |
Statistical analyses were performed using R, a system for statistical computation and graphics (Ihaka and Gentleman 1996; http://www.r-project.org). The RMA method in the oligo package from Bioconductor was used in R to summarize probe level data and to normalize the dataset to remove across array variation (Irizarry et al. 2003a,b;Bolstad et al., 2003). Log transformed data were used in subsequent analysis and plotting. To determine differentially expressed genes between control and knockdown, moderated T Statistics in limma (Smyth2004) was used. To adjust for multiple comparisons, p-values were adjusted using B-H method (Benjamini & Hochberg 1995) and genes with adjusted p-value <0.05 and absolute fold change >1.5 were considered potential targets for further investigation ['differentially_expressed.txt' on Series record].
|
| |
|
| Submission date |
Mar 28, 2012 |
| Last update date |
Mar 29, 2012 |
| Contact name |
Mihir Rajurkar |
| E-mail(s) |
[email protected]
|
| Phone |
5088563995
|
| Organization name |
UMASS Medical School
|
| Department |
Cancer Biology
|
| Lab |
Junhao Mao
|
| Street address |
364 Plantation st, 470Q LRB
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01604 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE36855 |
Gene expression analysis in Panc-1 cells in response to treatment with Gli3T, a dominant-negative repressor of Gli |
|
