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Series GSE11863 Query DataSets for GSE11863
Status Public on Aug 15, 2008
Title Differential expression of 24,426 human alternative splicing events and predicted cis-regulation in 48 tissues
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Alternative pre-messenger RNA splicing impacts development, physiology, and disease, but its regulation in humans is not well understood, partially due to the limited scale to which the expression of specific splicing events has been measured. We generated the first genome-scale expression compendium of human alternative splicing events using custom whole-transcript microarrays monitoring expression of 24,426 mutually exclusive alternative splicing event pairs in 48 diverse human samples. Over 11,700 genes and 9,500 splicing events were differentially expressed, providing a rich resource for studying splicing regulation. An unbiased, systematic screen of 21,760 4-mer to 7-mer words for cis-regulatory motifs identified 143 RNA 'words' enriched near regulated cassette exons, including six clusters of motifs represented by UCUCU, UGCAUG, UGCU, UGUGU, UUUU, and AGGG, which map to trans-acting regulators PTB, Fox, Muscleblind, CELF/CUG-BP, TIA-1, and hnRNP F/H, respectively. Each cluster showed a distinct pattern of genomic location and tissue specificity. For example, UCUCU occurs 110 to 35 nucleotides preceding cassette exons upregulated in brain and striated muscle but depleted in other tissues. UCUCU and UGCAUG appear to have similar function but independent action, occurring 5' and 3', respectively, of 33% of the cassette exons upregulated in skeletal muscle but co-occurring for only 2%.

Keywords: multiple tissue comparison
 
Overall design PolyA+ purified RNA pooled from multiple donors of a single human tissue type (e.g. cerebellum) were amplified with random primers and hybridized on a two-color ink-jet oligonucletodie microarray (17 array set) against a common reference pool, comprising ~20 normal adult tissue pools, on custom microarray patterns containing probes to monitor every exon and exon-exon junction in transcript databases, patent databases, and predicted from mouse transcripts. Data were analyzed for gene expression (the average of multiple probes), exon and junction expression, and splice form proportionality (see paper).
 
Citation(s) 18978788, 18794351
Submission date Jun 23, 2008
Last update date Mar 19, 2012
Contact name Amit V Kulkarni
E-mail(s) amit_kulkarni@merck.com
Phone 206-802-7352
Organization name Rosetta Inpharmatics / Merck Pharmaceuticals
Department Genomics
Lab Array Design
Street address 401 Terry Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (17)
GPL6826 Rosetta/Merck DT_Phase2_1_of_17 microarray
GPL6827 Rosetta/Merck DT_Phase2_2_of_17 microarray
GPL6828 Rosetta/Merck DT_Phase2_3_of_17 microarray
Samples (813)
GSM294996 Adipose vs pool
GSM294997 Adipose vs pool
GSM294998 Adipose vs pool
Relations
BioProject PRJNA105667

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
GSE11863_RAW.tar 128.9 Mb (http)(custom) TAR
Processed data included within Sample table
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