|
| Status |
Public on Jun 06, 2012 |
| Title |
Human D54 control 2 |
| Sample type |
RNA |
| |
|
| Source name |
D54
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Glioma cell
cell line: D54
transfection: control shRNA
|
| Growth protocol |
Fresh typsined cells seeding in DMEM/F12 and culture cellls overnight for RNA extract.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from 10^6 cells in 10-cm dish with Ambion RNAqueous Kit, according to the manufacturer’s instructions.
|
| Label |
None
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Vanderbilt Microarray Core Facility(FGSR).
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Description |
D54 transfected control shRNA
|
| Data processing |
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.
|
| |
|
| Submission date |
Feb 28, 2012 |
| Last update date |
Jun 06, 2012 |
| Contact name |
Miaojun Han |
| E-mail(s) |
[email protected]
|
| Organization name |
Vanderbilt University
|
| Street address |
1161 21st Ave S
|
| City |
nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE36116 |
Exon Level Expression Profiling in D54 with or without TIP-1 expression |
|
