|
| Status |
Public on Dec 01, 2007 |
| Title |
HeLa cells with siRNA specific for luciferase GL2, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Human cervical carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
siRNA, cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One day before transfection, HeLa cells were seeded in 6-well culture plates (1.5 x 10e5 cells per well) or 10-cm culture dishes (4.3 x 10e5 cells per dish). siRNA duplex (at a final concentration in culture medium of 30 nM) was transfected with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. siRNA duplices were from MWG Biotech (Ebersberg, Germany). Four days after siRNA transfection, total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).
|
| Label |
biotin
|
| Label protocol |
Ribosomal RNA was depleted from 1µg of total RNA using the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen Corp., Carlsbad, CA). cDNA was generated using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA) per manufacturer's instructions. cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labeling Kit (Affymetrix, Inc.).
|
| |
|
| Hybridization protocol |
Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45oC for 16 hours per manufacturers recommendation (see http://www.affymetrix.com/products/arrays/exon_application.affx for additional information). Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v. 1.4 to produce .CEL intensity files.
|
| Description |
Exon level expression
|
| Data processing |
.CEL files were background adjusted, quantile normalized netween all 12 samples and summarized in probeset level using RMAExpress. (http://rmaexpress.bmbolstad.com)
|
| |
|
| Submission date |
Aug 31, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Lee-Hsueh Hung |
| E-mail(s) |
Lee-Hsueh.Hung@chemie.bio.uni-giessen.de
|
| Phone |
0049-641-9935421
|
| Organization name |
University of Giessen
|
| Department |
Biochemistry
|
| Street address |
Heinrich-Buff-Ring 58
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE8945 |
Expression data from RNAi knockdown HeLa cells |
|
