|
| Status |
Public on Nov 26, 2007 |
| Title |
normal with no hydrocortisone treatment-5 |
| Sample type |
RNA |
| |
|
| Source name |
Primary culture of dermal fibroblasts from normal scar, no hydrocortisone treatment
|
| Organism |
Homo sapiens |
| Characteristics |
strain: 131
Disorder: normal
Condition: no hydrocortisone
|
| Treatment protocol |
Five strains each of cultured low-passage fibroblasts from keloids and normal scars were thawed from liquid nitrogen, subcultured and triplicate cultures grown to confluency (10 days) under standard culture conditions (daily feeding with Ham’s Nutrient Mixture F10 + 10% FBS) with and without 1.5 micromolar hydrocortisone.
|
| Growth protocol |
Five strains each of cultured low-passage fibroblasts from keloids and normal scars were thawed from liquid nitrogen, subcultured and triplicate cultures grown to confluency (10 days) under standard culture conditions (daily feeding with Ham’s Nutrient Mixture F10 + 10% FBS) with and without 1.5 micromolar hydrocortisone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a standard Trizol method with DNase treatment followed by a second Trizol extraction.
|
| Label |
biotin
|
| Label protocol |
Following quality control, the RNA was prepared for microarray analysis using the standard Affymetrix protocol (Affymetrix Inc, Santa Clara, CA). Briefly, a total of 5 µg of total RNA was reverse transcribed to double-stranded (ds) cDNA using an oligo-dT primer coupled to a T7 promoter. In vitro transcription from the ds cDNA was then carried out using T7 polymerase and incorporating biotin-modified CTP and UTP ribonucleotides.
|
| |
|
| Hybridization protocol |
Hybridized cRNA was detected using streptavidin coupled to phycoerythrin and visualized using GeneChip Scanner 3000 7G.
|
| Scan protocol |
GeneChips were scanned using GeneChip Scanner 3000 7G and GeneChip Operating System (GCOS, Affymetrix, Santa Clara, CA). Default values were used to grid images (.DAT) and generate .CEL and .CHP files and to generate gene expression values and ratios of gene expression between the hybridized samples
|
| Description |
Cell cultures were initiated from human biopsy material from normal dermal scars and keloids of adult males and females and frozen at first or second passage, in liquid nitrogen. Experimental cultures were derived from the first passage of cells thawed from liquid nitrogen.
|
| Data processing |
For statistical analysis, CEL files (raw Affymetrix data) were imported in GeneSpring 7.0 (Agilent Technologies) and transformed by RMA (Robust Multichip Analysis).
|
| |
|
| Submission date |
May 24, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Shirley Brody Russell |
| E-mail(s) |
shirley.b.russell@vanderbilt.edu
|
| Phone |
615-343-5853
|
| Fax |
615-343-8619
|
| Organization name |
Vanderbilt University
|
| Department |
Medicine
|
| Street address |
519 Light Hall
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232-0700 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7890 |
Gene profiling of keloid fibroblasts shows altered expression in multiple fibrosis-associated pathways |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE86362 |
| Reanalyzed by |
GSE119087 |
