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| 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
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| 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.
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| 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
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| 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 |
| E-mail(s) |
claire.darzacq@berkeley.edu
|
| Organization name |
UC Berkeley
|
| Department |
Molecular and Cell Biology
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| Lab |
Functional Imaging of Transcription
|
| Street address |
LI KA SHING Center
|
| City |
Berkeley |
| State/province |
California |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platforms (2) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA213182 |
| SRA |
SRP028190 |
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