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Series GSE28475 Query DataSets for GSE28475
Status Public on Apr 03, 2012
Title Genome-wide Expression Assay Comparison Across Frozen and Fixed Postmortem Brain Tissue Samples
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Comparison between in vitro transcription- and cDNA-mediated annealing, selection and ligation (DASL)-based assays on brain-specific reference RNA, and postmortem frozen and formalin fixed brain tissue from autistic and control cases. Investigation of data preprocessing techniques for DASL-assayed RNA samples from frozen brain tissue.
Overall design IVT- and DASL-based expression assays were performed on 10 reference RNA samples (brain and pooled artificially degraded at 0, 10, 30, and 60 min), 4 formalin-fixed tissue-extracted RNA samples with replicates, and 57 frozen tissue-extracted RNA samples with replicates. A subset of the 57 (N=33 samples) from frozen brain tissue assayed using the DASL-based platform were then used to test different dataset preprocessing strategies implemented in the lumi package in R/Bioconductor. The data from frozen-tissue extracted DASL-processed RNA samples passing exclusion criteria were log2 transformed and normalized using quantile normalisation with lumi in R (quantile-normalized data available as a supplementary file linked to the Series record).
Contributor(s) Chow ML, Li H, Winn ME, April C, Carter Barnes C, Fan J, Wynshaw-Boris A, Fu X, Courchesne E, Schork NJ
Citation(s) 22375143, 21906392
Submission date Apr 08, 2011
Last update date Sep 24, 2019
Contact name Maggie Chow
Phone 858-534-6905
Organization name NIH-UC San Diego Autism Center of Excellence
Department Neuroscience
Street address 8110 La Jolla Shores Dr. Ste 201
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
Platforms (2)
GPL6883 Illumina HumanRef-8 v3.0 expression beadchip
GPL13388 Illumina Human 12k DASL assay
Samples (143)
GSM703645 Frozen Tissue_DASL_57B rep1
GSM703646 Frozen Tissue_DASL_61B
GSM703647 Frozen Tissue_DASL_64B
BioProject PRJNA139321

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
GSE28475_RAW.tar 3.9 Mb (http)(custom) TAR
GSE28475_quantile_normalized.txt.gz 6.4 Mb (ftp)(http) TXT
Processed data are available on Series record

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