|
| Status |
Public on May 15, 2014 |
| Title |
mock transfected cells, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mock transfected cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
transfection: mock
|
| Treatment protocol |
Cells were transfected with 3nM siRNA/ siPool or mock transfected with Lipofectamine RNAiMax according to the manufacturers protocol
|
| Growth protocol |
Cells were grown under standard conditions in DMEM 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed 48h after transfection according to the manufacturer's instructions (Nucleospin RNA, Machery Nagel).
|
| Label |
biotin
|
| Label protocol |
The Ambion WT Expression Kit Protocol was used for the preparation of biotinylated sense-strand cDNA from 300ng of total RNA, followed by fragmentation and labeling according to the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).
|
| |
|
| Hybridization protocol |
3.8 μg of fragmented and labeled sense-strand cDNA were hybridized for 16 h at 45°C on GeneChip Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).
|
| Description |
Gene expression data from mock transfected cells
|
| Data processing |
The raw intensities of the CEL files were normalized with RMA.
|
| |
|
| Submission date |
May 13, 2014 |
| Last update date |
Jun 04, 2014 |
| Contact name |
Julia C Engelmann |
| E-mail(s) |
julia.engelmann@ur.de
|
| Organization name |
University of Regensburg
|
| Department |
Statistical Bioinformatics
|
| Street address |
Josef-Engert-Str. 9
|
| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16686 |
| Series (2) |
| GSE57646 |
siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects (HuGene-2_0) |
| GSE57674 |
siPools: highly complex but accurately defined siRNA pools eliminate Off-target effects |
|
