|
| Status |
Public on Sep 10, 2019 |
| Title |
genomic DNA from normotrophic scar fibroblasts from patient 3 |
| Sample type |
genomic |
| |
|
| Source name |
Patient 3 Scar
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age (years): 19
time since injury (years): 2
|
| Treatment protocol |
There were no treatments applied to the scar and control cells in vitro. DNA was bisulfite treated prior to processing on the chip
|
| Growth protocol |
3mm punch biopsies were taken from the forearm scar site and a matched site on the uninjured forearm by the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until passage 2, at which point DNA and RNA was extracted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using either the Promega Wizard SV Genomic DNA system (Patients 1 and 2, Promega, USA) or the QIAamp DNA mini kit system (Patients 3-6, Qiagen, Netherlands) as per manufacturer’s instructions
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
Normotrophic Scar Fibroblast DNA
|
| Data processing |
Methylation data was imported from the raw files using Illumina® GenomeStudio and analysed using R statistics software, using the RnBeads package
|
| |
|
| Submission date |
Sep 09, 2019 |
| Last update date |
Sep 10, 2019 |
| Contact name |
Andrew William Stevenson |
| E-mail(s) |
andrew.stevenson@uwa.edu.au
|
| Phone |
864887515
|
| Organization name |
University of Western Australia
|
| Department |
School of Biomedical Sciences
|
| Lab |
Burn Injury Research Unit
|
| Street address |
Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA
|
| City |
Crawley |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE137134 |
A methylation analysis of human normotrophic scar dermal fibroblasts |
|
