|
| Status |
Public on Jun 24, 2014 |
| Title |
GBCs P3 biol. repl.6 |
| Sample type |
RNA |
| |
|
| Source name |
GBCs just after calyx of Helds formation
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
strain: Sprague Dawley
age: P03
cell type: globular bushy cells just after calyx of Helds formation
|
| Treatment protocol |
Brains were acutely removed and flash frozen on dry ice. Labelled cells were excised from cryosections by laser microdissection.
|
| Growth protocol |
Rats were stereotaxically injected with Cholera toxin B and sacrificed 24h later
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from laser microdissection dissected cells using the RNeasy Micro Kit (Qiagen) according to the manufacturers instructions and precipitated by adding 0.3M Na-acetate and ethanol. Total RNA was linearly amplified over two rounds using MessageAmp II aRNA Amplification Kit (Ambion).
|
| Label |
biotin
|
| Label protocol |
Biotin-labelled NTPs were introduced in the second round of RNA amplification.
|
| |
|
| Hybridization protocol |
10µg aRNA were hybridized to Affymetrix Rat Expression 230 2.0 chips. Hybridization and labeling were performed by an authorized Affymetrix service provider (Atlas Biolabs GmbH, Friedrichstr.127, 10117 Berlin, Germany).
|
| Scan protocol |
Scanning was performed by an authorized Affymetrix service provider (Atlas Biolabs GmbH, Friedrichstr.127, 10117 Berlin, Germany).
|
| Description |
Gene expression of P03 GBCs
|
| Data processing |
The R – Bioconductor open source software platform was used throughout the whole data analysis workflow. Quality of obtained microarray data was assessed using the ‘arrayQualityMetrics’ library. Background correction and normalization of raw expression values were performed using of the ‘gcrma’ algorithm. A moderate t-test based on Bayesian statistics, which allows for the reliable estimation of standard deviation of few replicates, was chosen for primary data analysis, and resulting p-values were corrected for multiple test-ing using the false discovery rate method (FDR) of Benjamini and Hochberg (1995).
|
| |
|
| Submission date |
Aug 06, 2013 |
| Last update date |
Jun 24, 2014 |
| Contact name |
Christoph Koerber |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Heidelberg
|
| Department |
Institute of Anatomy and Cell Biology
|
| Street address |
Im Neuenheimer Feld 307
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE49599 |
Expression profiles of globular bushy cells (GBCs) during maturation |
|
