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Series GSE76902 Query DataSets for GSE76902
Status Public on Jun 21, 2016
Title EventPointer: An effective identification of alternative splicing events using junction arrays
Organism Homo sapiens
Experiment type Expression profiling by array
Summary There is an increasing interest on the role of Alternative splicing (AS) in different pathologies. The Affymetrix Human Transcriptome Array (HTA 2.0) can be used to explore AS very efficiently. However, the interpretation software provided by its vendor (TAC 3.0) does not fully exploit its potential and can only be applied to case-control studies. EventPointer is an R package to identify Alternative Splicing events using HTA 2.0 arrays. It can be applied to complex experimental designs. The software provides a list of the detected events indicating the type of event (cassette, alternative 3’, etc.), their statistical significance, and affected protein domains affected. The false positive rate is very low (the first detected false positive was ranked in the 149th position). EventPointer is publicly available at GitHub.
 
Overall design 9 samples with 3 replicates from A549 lung adenocarcinoma cell lines. The experiment includes 3 conditions: Cells treated with the transfection vehicle (Lipofectamine), cells treated with scrambled RNA and cells transfected with a siRNA that targets SRSF1
Web link https://github.com/jpromeror/EventPointer
 
Contributor(s) Romero JP, Muniategui A, de Miguel F, Aramburu A, Montuenga L, Pio R, Rubio A
Citation(s) 27315794
Submission date Jan 15, 2016
Last update date Jun 23, 2016
Contact name Juan Pablo Romero
E-mail(s) jromeror@unav.es
Organization name CIMA
Department Hemato-Oncology
Lab Advanced Genomics
Street address Av. de Pío XII, 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platforms (1)
GPL21339 [HTA-2_0] Affymetrix Human Transcriptome Array 2.0 (probesets grouped by R EventPointer package)
Samples (27)
GSM2040329 Cells trated with Lipofectamine sample 1 replicate 1
GSM2040330 Cells trated with Lipofectamine sample 1 replicate 2
GSM2040331 Cells trated with Lipofectamine sample 1 replicate 3
Relations
BioProject PRJNA308905

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
GSE76902_RAW.tar 669.2 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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