NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4067491 Query DataSets for GSM4067491
Status Public on Sep 10, 2019
Title genomic DNA from normotrophic scar fibroblasts from patient 5
Sample type genomic
 
Source name Patient 5 Scar
Organism Homo sapiens
Characteristics Sex: Male
age (years): 25
time since injury (years): 5
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

Data table header descriptions
ID_REF
VALUE Average Beta or normalized (provide the normalization method) Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.3082323 0
cg00000108 0.9028472 0
cg00000109 0.6265647 0
cg00000165 0.3788856 0
cg00000236 0.77429 0
cg00000289 0.5678571 0
cg00000292 0.58051 0
cg00000321 0.2901786 0
cg00000363 0.3046823 0
cg00000622 0.02272727 0
cg00000658 0.8394988 0
cg00000714 0.1949087 0
cg00000721 0.8706564 0
cg00000734 0.1233459 0
cg00000769 0.06972928 0
cg00000807 0.8082811 0
cg00000884 0.7531462 0
cg00000905 0.2140637 0
cg00000924 0.6235884 0
cg00000948 0.8021567 0

Total number of rows: 485577

Table truncated, full table size 10972 Kbytes.




Supplementary file Size Download File type/resource
GSM4067491_9221198158_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM4067491_9221198158_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Raw data provided as supplementary file
Processed data included within Sample table
Raw data are available on Series record

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