|
| Status |
Public on Jan 01, 2008 |
| Title |
HeLa shRHAU+ STV 3 |
| Sample type |
RNA |
| |
|
| Source name |
HeLa shRHAU+ STV 3
|
| Organism |
Homo sapiens |
| Characteristics |
Strain: HeLa
Gender: Female
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNeasy kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Total RNA (5 μg) from each replicate was reverse transcribed and labelled using the Affymetrix 1-cycle labelling kit as per manufacturer’s instructions. Biotinylated cRNA (20 μg) was fragmented by heating with magnesium (as per Affymetrix’s instructions)
|
| |
|
| Hybridization protocol |
15 μg of fragmentated cRNA was hybridized to Human U133 plus 2.0 GeneChipsTM
|
| Scan protocol |
The chips were scanned using an Affymetrix 7G scanner.
|
| Description |
This is the sample of HeLa-shRHAU cells with expression of short hairpin RNA, cultured 24 hrs in serum-depleted medium
|
| Data processing |
GC-RMA expression values and detection P-values were estimated using Refiner 4.0 from Genedata AG (Basel, Switzerland). Data analysis was performed using Analyst 4.0 from Genedata AG (Basel, Switzerland). The chip distributions were standardized by quantile normalization and they were scaled to make the median expression value 500. For the analysis of steady-state RNA levels, genes were required to have a detection p-value < 0.04 (Affymetrix default) in at least two replicates of any one condition.The objective was to exclude genes that are not expressed in any condition. They were then subjected to a student t-test (P<0.05) and have a median fold change of 1.5 or 2 greater between samples dox+ and dox- or with and without starvation.
|
| |
|
| Submission date |
Jun 13, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Fumiko Iwamoto |
| E-mail(s) |
fumiko@fmi.ch
|
| Organization name |
FMI
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE8192 |
The DExH-box RNA helicase RHAU is a Nuclear Protein Involved in Transcription and mRNA Decay |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
