 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 26, 2015 |
| Title |
RNA-seq analysis reveals significant effects of EGFR signaling on mesenchymal stem cells (MSC) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to analyse the whole transcriptome of MSCs stimulated with TGFα in order to comprehensively assess the genes regulated by EGFR signalling
Methods: Libraries of cDNA were obtained from poly(A)-RNA fractions from not-stimulated or TGFα-stimulated MSCs and sequenced with a SOLiD 5500xl platform. Whole-transcriptome reads were aligned to the version 19 of the human genome (hg19) with the SOLiD LifeScope Genomic Analysis Software version 2.5 (Life Technologies) using the parameters recommended in the user’s manual. The number of observed counts (number of reads/gene) was normalized for the length of the transcript and the number of mapped reads (RPKM) (Reads Per Kilobase per Million of mapped reads). DESeq tool in R package was used to obtain a statistical evaluation of differential gene expression.
Results: 1,640 genes resulted highly differentially regulated: 967 genes up-regulated with Fold Induction (FI)≥1.50, and 673 genes down-regulated with FI≤0.50. When highly regulated genes were categorized into enriched categories according to GO molecular function classification and KEGG pathways analysis, a large number of genes coding for potentially secreted proteins or for surface receptors resulted enriched following TGFα treatment. In particular, significant up-regulation of VEGFA, IL6, EREG, HB-EGF, LIF, NGF, NRG1, CCL19, CCL2, CCL25 and CXCL3 was observed.
Conclusions: Taken together these findings suggest that EGFR activation in MSCs leads to a significant change in the expression of a wide array of genes coding for secreted proteins that can significantly enhance tumor progression by acting on several mechanisms within the tumor microenvironment
|
| |
|
| Overall design |
mRNA profiles of MSCs starved overnight in serum free medium and treated for 1 hour with recombinant at a concentration of 10 ng/ml by deep sequencing, in quadruplicate, using SOLiD 5500xl.
|
| |
|
| Contributor(s) |
Normanno N, DeLuca A, Bergantino F, Costantini S |
| Citation(s) |
25344915 |
| |
| Submission date |
Aug 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicola Normanno |
| Organization name |
INT PASCALE
|
| Street address |
via Mariano Semmola
|
| City |
Naples |
| ZIP/Postal code |
80138 |
| Country |
Italy |
| |
|
| Platforms (1) |
| GPL16288 |
AB 5500xl Genetic Analyzer (Homo sapiens) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA258540 |
| SRA |
SRP045636 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60560_RAW.tar |
1.0 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
Less...
More...