|
| Status |
Public on Dec 18, 2008 |
| Title |
relA-/-_0h_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse tissue, relA-/-, 0h
|
| Organism |
Mus musculus |
| Characteristics |
mouse embryonic fibroblasts (MEF)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total cellular RNA was isolated using RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers instructions, possible contamination by genomic DNA was removed by DNAseI treatment using the RNAse-Free DNAse Set (Qiagen), quality was checked by spectrophotometry and agarose gel electrophoresis, 2µg RNA per sample was used for cDNA preparation when A260:A280 ratio was 1.8-2.1 and RNA was intact
|
| Label |
biotin
|
| Label protocol |
Standard Codelink protocol (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)
|
| |
|
| Hybridization protocol |
Standard Codelink protocol (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)
|
| Scan protocol |
using GenePix 4000B Array Scanner and GenePix Pro 4.0 software according to the settings suggested by GE Healthcare (supplier of CodeLink microarrays at experiment time, http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)
|
| Description |
no additional information
|
| Data processing |
Raw data were analysed using Codelink Expression Analysis v.4.1 software to extract MDFCs (minimal detectable fold changes). Subsequent analysis was done using R and Bioconductor. Only probes with probe type „DISCOVERY“ and no MSR (Manufactory Slide Report) flag were used, leaving 19580 genes. Intensity values <0.01 were set to 0.01. Raw intensities were scaled to array median. After log2-transformation, quantile normalization was applied across all arrays.
|
| |
|
| Submission date |
Jul 02, 2008 |
| Last update date |
Dec 18, 2008 |
| Contact name |
Daniela Albrecht |
| E-mail(s) |
[email protected]
|
| Organization name |
BioControl Jena GmbH
|
| Street address |
Wildenbruchstr. 15
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL5979 |
| Series (1) |
| GSE11963 |
RelA and RelB-dependent transcriptome analysis in lymphotoxin-ß receptor stimulated mouse embryonic fibroblasts |
|
