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Series GSE17403 Query DataSets for GSE17403
Status Public on Jul 18, 2011
Title Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by genome tiling array
Expression profiling by high throughput sequencing
Summary Epidermal growth factor (EGF) is a key regulatory growth factor activating a myriad of processes affecting cell proliferation and survival that are relevant to normal development and disease. Here we have used a combined approach to study the EGF dependent transcriptome of HeLa cells. We obtained mRNA expression profiles using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, Febit, and Illumina) in combination with digital gene expression profiling (DGE) with the Illumina Genome Analyzer I (GA-I). By applying a procedure for cross-platform data meta-analysis based on rank product and global ancova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We used this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we found a whole new set of genes previously unrelated to the currently accepted EGF associated cellular functions, among which are metallothionein genes. We propose the use of global genomic cross-validation to generate more reliable datasets derived from high content technologies (microarrays or deep sequencing). This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.

Keywords: treated vs. untreated comparison, time course
 
Overall design Time course experiment comparing HeLa gene expression in response to EGF analyzed on different microarray platforms (Agilent, IMPPC, Illumina, and Operon) and by digital gene expression using short read high throughput tag sequencing. Three independent experiments were performed where HeLa cells were serum deprived for 24 hours and were either left untreated or treated with EGF for 6, and 24 h and harvested for RNA extraction. Technical dye swap duplicates were performed for each of the three biological replicates in both time points.

Comparative genomic hybridization of HeLa cell genomic DNA versus poooled genomic DNA from blood obtained from human females conducted on commercial oligonucleotide microarrays (Human Genome CGH Microarray Kit 244A, Agilent Technologies) in order to assess DNA dosage dependence of gene expression levels and response to EGF.

Digital gene expression using short read high throughput tag sequencing data submitted to NCBI's SRA
 
Contributor(s) Llorens F, Hummel M, Pastor X, Ferrer A, Mosquera AM, Iraola S, Gonzalez E, Lozano J, Sumoy L
Citation(s) 21699700
Submission date Jul 29, 2009
Last update date May 15, 2019
Contact name Lauro Sumoy
E-mail(s) lsumoy@igtp.cat
Organization name IGTP
Department High Content Genomics and Bioinformatics
Street address Ctra. Can Ruti, Camí de les escoles s/n
City Badalona
State/province Barcelona
ZIP/Postal code 08916
Country Spain
 
Platforms (6)
GPL4091 Agilent-014693 Human Genome CGH Microarray 244A (Feature number version)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
GPL6102 Illumina human-6 v2.0 expression beadchip
Samples (60)
GSM434627 6h EGF versus Control replicate 1 (Agilent)
GSM434628 6h EGF versus Control replicate 1 dye swap (Agilent)
GSM434629 6h EGF versus Control replicate 2 (Agilent)
Relations
SRA SRP002184
BioProject PRJNA118851

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
GSE17403_RAW.tar 1.3 Gb (http)(custom) TAR (of FA, GPR, TSV, TXT)
GSE17403_Solexa_counts_3samples_RefSeq_collapsed_tab.txt.gz 623.7 Kb (ftp)(http) TXT
GSE17403_Solexa_counts_3samples_RefSeq_nonfiltered_tab.txt.gz 1.9 Mb (ftp)(http) TXT
GSE17403_illumina_non-normalized.txt.gz 13.0 Mb (ftp)(http) TXT
GSE17403_illumina_normalized.txt.gz 6.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data included within Sample table
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Processed data are available on Series record
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