GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE49159 Query DataSets for GSE49159
Status Public on Dec 16, 2015
Title mRNA differential expression analysis in a human ex vivo model of chronic wounds
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To study the fibroblast to myofibroblast differentiation in a normal or pathological situation, NHDF (Normal human dermal fibroblast) obtained from two different healthy donors (donors A and B) were either left untreated (T-E-) either treated with TGF-beta alone (T+E-), or with exudate from chronic wounds (T-E+) or both (T+E+). For each different treatment we performed mRNA deep sequencing 3 times : twice with cells from donor A and once with cells from donor B.We focused our study on gene expression profile as a representation of cell fate. We performed mRNA deep sequencing analysis of the 4 different conditions. For each condition, mRNA deep sequencing was performed 3 times : twice with cells from donor A and once with cells from donor B.Comparing the mRNA abundance between the different treatments, we identified 3 lists of genes characterizing the different gene expression states: 171 genes in List I representing the genes differentially expressed during normal fibroblast to myofibroblast differentiation, 409 genes in List II representing the genes differentially expressed upon exudate-only treatment and 1006 genes in List III representing the genes differentially expressed upon the combination of exudate and TGF-beta treatments.
Overall design 4 different treatments are compared : (T-E-) NHFD left untreated, (T+E-) NHDF treated with TGFbeta for 4 days, (T-E+) NHDF treated with exudate for 4 days and (T+E+) NHDF treated with both TGFbeta and exudate. NHDF : Normal Human Dermal Fibroblast
Contributor(s) Noizet M, Lagoutte E, Gratigny M, Bouschbacher M, Lazareth I, Roest Crollius H, Darzacq X, Dugast-Darzacq C
Citation(s) 26663515
Submission date Jul 24, 2013
Last update date May 26, 2023
Contact name Claire Dugast-Darzacq
Organization name UC Berkeley
Department Molecular and Cell Biology
Lab Functional Imaging of Transcription
Street address LI KA SHING Center
City Berkeley
State/province California
ZIP/Postal code 94720
Country USA
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM1194803 GLD-1
GSM1194804 GLD-2
GSM1194805 GLD-7
BioProject PRJNA213182
SRA SRP028190

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
GSE49159_RPKM_values.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap