|
| Status |
Public on Feb 01, 2013 |
| Title |
CHIR rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Rat XEN cells cultured 2 days with inhibitor of GSK3 kinase
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Fisher
cell type: Rat XEN cells
treated with: 3 μM CHIR99021 (Axon Medchem)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA were extracted by RNA mini kit (Qiagen), residual genomic DNA was removed by DNAse I treatment (Qiagen).
|
| Label |
biotin
|
| Label protocol |
ssDNA was labelled usind WT terminal labeling kit (Affymetrix)
|
| |
|
| Hybridization protocol |
labelled ssDNA was hybridized with Hybridization Wash and Stain kit (Affymetrix).
|
| Scan protocol |
Gene Chip Scanner 7G, command console software AGCC
|
| Description |
ILC--04-CHIR-070610-RatGe-St1-0.CEL
|
| Data processing |
Arrays have been quantile-normalize with respect to the probe GC content using the RMA algorithm (GC contend adjustment, RMA background correction and mean probe set summarization) using Partek Genomic Suite (v.6.3). After normalization the arrays have been checked for outlier using the principal component analysis using a correlation dispersion matrix and normalized Eigenvector scaling. Differential expression of summarized gene level expression was calculated using the Partek ANOVA statistic followed by a FDR multiple testing correction. Differences between individual pairs ofconditions have been calculated using the LSD post hoc test.
|
| |
|
| Submission date |
Nov 21, 2012 |
| Last update date |
Feb 02, 2013 |
| Contact name |
Ilya Chuykin |
| E-mail(s) |
ilya.chuykin@mdc-berlin.de
|
| Phone |
+4915129016374
|
| Fax |
+493094062518
|
| Organization name |
Max-Delbruck Center for Molecular Medicine
|
| Department |
Molecular Biology of Peptide Hormones
|
| Lab |
Michael Bader
|
| Street address |
Robert-Rossle str 10
|
| City |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10741 |
| Series (1) |
| GSE42438 |
PTHRP/Adenylate cyclase promotes parietal whereas Wnt/β-catenin signaling promotes visceral endoderm differentiation of rat XEN cells. |
|
