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Series GSE17468 Query DataSets for GSE17468
Status Public on Aug 15, 2009
Title The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate alternative splicing events
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2) are recently discovered epithelial-specific RNA-binding proteins that promote splicing of the epithelial variant of the FGFR2, ENAH, CD44, and CTNND1 transcripts. To catalogue a larger set of splicing events under the regulation of the ESRPs, we profiled splicing changes induced by RNA interference-mediated knockdown of ESRP1 and ESRP2 expression in a human epithelial cell line using the splicing-sensitive Affymetrix Exon ST1.0 Arrays. Analysis of the microarray data using the previously described MADS tool resulted in the identification of over a hundred candidate ESRP-regulated splicing events. We were able to independently validate 37 of these targets by RT-PCR. The ESRP-regulated events encompass all known types of alternative splicing events. Importantly, a number of these regulated splicing events occur in gene transcripts that encode proteins with well-described roles in the regulation of actin cytoskeleton organization, cell-cell adhesion, cell polarity, and cell migration. In sum, this work reveals a novel list of transcripts differentially spliced in epithelial and mesenchymal cells, implying that coordinated alternative splicing plays a critical role in determination of cell type identity.

Keywords: control / knockdown comparison
 
Overall design Short interfering knockdown of ESRP1 and ESRP2 in human PNT2 prostatic epithelium cells was performed as described before (Warzecha et al., 2009, Molecular Cell 33:591-601). The efficiency of ESRP1 and ESRP2 knockdown was monitored by quantitative RT-PCR as described before (Warzecha et al., 2009, Molecular Cell 33:591-601). In all cases the efficiency of the knockdown was close to 80%. We conducted Exon array profiling on RNAs from four siESRP1/2-treated samples and four siGFP controls.
 
Contributor(s) Warzecha CC, Shen S, Xing Y, Carstens RP
Citation(s) 19829082
Submission date Aug 02, 2009
Last update date Feb 18, 2019
Contact name Yi Xing
E-mail(s) yi-xing@uiowa.edu
Phone 319-384-3099
Fax 319-384-3150
Organization name University of Iowa
Department Internal Medicine, Biomedical Engineering
Street address 3294 CBRB, 285 Newton Rd
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platforms (1)
GPL5175 [HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
Samples (8)
GSM435813 PNT2-siGFP, rep1
GSM435814 PNT2-siGFP, rep2
GSM435815 PNT2-siGFP, rep3
Relations
BioProject PRJNA118751

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
GSE17468_RAW.tar 178.1 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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