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Sample GSM1202443 Query DataSets for GSM1202443
Status Public on Jun 24, 2014
Title GBCs P21 biol. repl. 5
Sample type RNA
 
Source name GBCs when calyx is fully mature
Organism Rattus norvegicus
Characteristics tissue: brain
strain: Sprague Dawley
age: P21
cell type: globular bushy cells when calyx is fully mature
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 P21 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) koerber@ana.uni-heidelberg.de
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

Data table header descriptions
ID_REF
VALUE GC-RMA signal
ABS_CALL
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 63.2 P 0.004998
AFFX-BioB-M_at 88.5 P 0.000095
AFFX-BioB-3_at 55.8 P 0.00141
AFFX-BioC-5_at 147.3 P 0.000127
AFFX-BioC-3_at 197.9 P 0.00007
AFFX-BioDn-5_at 309.6 P 0.000225
AFFX-BioDn-3_at 763.2 P 0.000446
AFFX-CreX-5_at 1823.7 P 0.000052
AFFX-CreX-3_at 1666.6 P 0.000044
AFFX-DapX-5_at 3.4 A 0.0727
AFFX-DapX-M_at 2.1 A 0.48511
AFFX-DapX-3_at 1.2 A 0.631562
AFFX-LysX-5_at 8 A 0.0727
AFFX-LysX-M_at 0.9 A 0.51489
AFFX-LysX-3_at 1.3 A 0.195266
AFFX-PheX-5_at 0.7 A 0.852061
AFFX-PheX-M_at 0.4 A 0.904333
AFFX-PheX-3_at 8 A 0.559354
AFFX-ThrX-5_at 0.9 A 0.760937
AFFX-ThrX-M_at 0.6 A 0.672921

Total number of rows: 31099

Table truncated, full table size 812 Kbytes.




Supplementary file Size Download File type/resource
GSM1202443_Sygnis9.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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