|
| Status |
Public on Jun 22, 2017 |
| Title |
Donor N4, control |
| Sample type |
RNA |
| |
|
| Source name |
fibroblasts isolated from skin biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
donor: N4
treatment: DMSO
|
| Treatment protocol |
24h treatment with 50uM dimethyl fumarate (DMF,D) or DMSO(C) +/- 2.5ng/ml TGFb(T)
|
| Growth protocol |
Human dermal skin fibroblasts were grown to confluency in DMEM+10%FBS. Medium was changed to serum free 16h before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol reagent and ethanol precipitation
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from dermal fibroblasts treated with DMSO for 24h.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite (version 2.12), using R version 2.15.1 and the Brainarray hugene20sthsentrezg R package (version 17.0.0) (http://mbni.org/customcdf/17.0.0/entrezg.download/hugene20st_Hs_ENTREZG_17.0.0.zip).
|
| |
|
| Submission date |
Jun 23, 2016 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL17930 |
| Series (1) |
| GSE83642 |
Effect of dimethyl fumarate (DMF) and transforming growth factor (TGFb) on gene expression in dermal fibroblasts |
|
