|
| Status |
Public on Oct 20, 2009 |
| Title |
HEK293E cells, TDP-43 siRNA, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
HEK cells transfected with TDP-43 siRNA, 24h after transfection
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293E
|
| Treatment protocol |
Cells were transiently transfected three consecutive days using HiPerfect with 5nmol scrambled (both Qiagen) or TDP-specific siRNAs (5’-CAATAGCAATAGACAGTTA-3’) and cultivated for 24h.
|
| Growth protocol |
HEK293E cells were grown in Dulbecco’s modified Eagle medium (DMEM) (Biochrom) supplemented with 10% fetal bovine serum (PAA) at 37°C under humidified 5% CO2/air
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using RNeasy Mini Kit (Qiagen) following manufacturers instructions for animal cells.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner.
|
| Description |
NA
|
| Data processing |
The data were analysed using GC-RMA for background correction, normalization and probe summarization using the Bioconductor package gcrma with default values.
|
| |
|
| Submission date |
Oct 19, 2009 |
| Last update date |
Oct 19, 2009 |
| Contact name |
Michael H. Walter |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Tuebingen
|
| Department |
Department of Medical Genetics
|
| Lab |
The Microarray Facility Tübingen
|
| Street address |
Calwer Str. 7
|
| City |
Tuebingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE18632 |
Knockdown of transactive response DNA-binding protein TDP-43 downregulates histone deacetylase 6 |
|
