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Series GSE8349 Query DataSets for GSE8349
Status Public on Mar 25, 2008
Title Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice
Organism Mus musculus
Experiment type Expression profiling by array
Summary The aim of the present study was to compare, on a statistical basis, the performance of different microarray platforms to detect differences in gene expression in a realistic and challenging biological setting. Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina and home-spotted oligonucleotide arrays. We observed considerable overlap between the different platforms, the overlap being better detectable with significance level-based ranking than with a p-value based cut-off. Confirming the qualitative agreement between platforms, Pathway analysis consistently demonstrated aberrances in GABA-ergic signalling in the transgenic mice, even though pathways were represented by only partially overlapping genes on the different platforms.
Keywords: microarray platform comparison
 
Overall design 5 biological replicates for each experimental group were analyzed on each of the five platforms. For two-color arrays a dye swap was performed.

ABI_raw_data.csv contains the raw data for GSM206638 to GSM206647.
Illumina_raw_data.csv contains the raw data for GSM206887 to GSM206896. In these files, the sample identifiers are included in the column headers.
 
Contributor(s) 't Hoen PA, Pedotti P
Citation(s) 18331641, 18927111
Submission date Jul 02, 2007
Last update date Feb 11, 2019
Contact name Peter A.C. 't Hoen
E-mail p.a.c.hoen@lumc.nl
Phone +31 71 5269421
Fax +31 71 5268285
URL http://www.humgen.nl
Organization name Leiden University Medical Center
Department Center for Human and Clinical Genetics
Street address PO Box 9600
City Leiden
ZIP/Postal code 2300 RC
Country Netherlands
 
Platforms (5)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
GPL2872 Agilent-012694 Whole Mouse Genome G4122A (Feature Number version)
GPL2995 ABI Mouse Genome Survey Microarray
Samples (50)
GSM206607 WT hippocampus 1 (Affymetrix)
GSM206608 WT hippocampus 2 (Affymetrix)
GSM206609 WT hippocampus 3 (Affymetrix)
Relations
BioProject PRJNA101361

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE8349_ABI_raw_data.csv 3.0 Mb (ftp)(http) CSV
GSE8349_RAW.tar 209.9 Mb (http)(custom) TAR (of CEL, GPR, TXT)
GSE8349_illumina_raw_data.csv 26.5 Mb (ftp)(http) CSV
Raw data provided as supplementary file
Raw data is available on Series record
Processed data included within Sample table

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