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Series GSE104973 Query DataSets for GSE104973
Status Public on Sep 05, 2018
Title Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm [RNA-Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. Common results and discrepancies between both technologies were validated or resolved by more than 200 PCRs.
 
Overall design Three different triple negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, SUM 149) treated with CX4945 and DMSO with 5 replicates. A total of 30 samples
 
Contributor(s) Romero JP, Ortiz-Estévez M, Muniategui A, Carrancio S, de Miguel FJ, Carazo F, Montuenga L, Trotter M, Loos R, Pío R, Rubio A
Citation(s) 30253752
Submission date Oct 14, 2017
Last update date May 15, 2019
Contact name Juan Pablo Romero
E-mail(s) juanpablo.romerorioj@10xgenomics.com
Organization name 10x Genomics
Department Computational Biology
Street address 6230 Stoneridge Mall Rd
City Pleasanton
State/province CA
ZIP/Postal code 94588
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (30)
GSM2811267 MDA231 cell line treated with CX4945 Replicate 1
GSM2811268 MDA231 cell line treated with CX4945 Replicate 2
GSM2811269 MDA231 cell line treated with CX4945 Replicate 3
This SubSeries is part of SuperSeries:
GSE104974 Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm
Relations
BioProject PRJNA414291
SRA SRP119952

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
GSE104973_Processed_FPKM.txt.gz 16.4 Mb (ftp)(http) TXT
GSE104973_Processed_RawCounts.txt.gz 3.5 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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