|
| Status |
Public on Jan 07, 2020 |
| Title |
T2DR [DR259] |
| Sample type |
genomic |
| |
|
| Source name |
Blood, T2DR
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
disease group: Type-2 Diabetes with proliferative retinopathy
phenotype: Pan retinal photocoagulation with non-neovascularization and Non-diabetic macular edema in both eyes
blood glucose: HbA1C: 8.1%.
bmi (kg/m2): 27.8
duration (yr): 17
age (yr): 73
gender: male
population: Taiwanese
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
The patients have been diagnosed with resulting to classified groups as Control, Type-2 diabetes with non-complication (T2D), Type-2 diabetes with nephropathy (T2DN), Type-2 diabetes with non-proliferative retinopathy (T2NPDR) and Type-2 diabetes with proliferative retinopathy (T2PDR). The blood samples were collected individually for the only research purposes with their voluntary participation. Whole blood of these samples was contained individually in the EDTA tubes for further steps of array analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The MethylMiner Methylated DNA Enrichment Kit (Invitrogen) was used to isolate the methylated DNA. One microgram of genomic DNA was sonicated to 100–500 bp. Then 3.5 mg (7 mL) of MBD-Biotin Protein was coupled to 10 mL of Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
The 50 ng of methylated DNA from MeDIP immunoprecipitations and MBD-Capture reactions was amplified with GenomePlex Single Cell Whole Genome Amplification Kit (Sigma, Catalog No. WGA4) in each amplification performance was instructed by the company protocol. Then, cDNA was purified using cDNA cleanup columns (Affymetrix, Catalog No. 900371), and 7.5 ug of amplified DNA was fragmented and labeled following Affymetrix Chromatin Immunoprecipitation Assay Protocol (P/N: 702238 Rev. 3).
|
| |
|
| Hybridization protocol |
The hybridization was performed against the Affymetrix GeneChip® Human Promoter 1.0R array by following the Affymetrix protocol for 17 hours at 45oC and 60 rpm.
|
| Scan protocol |
The arrays were subsequently washed (Affymetrix Fluidics Station 450) and stained with streptavidin-phycoerythrin (GeneChip® Hybridization, Wash, and Stain Kit, 900720), and were scanned on an Affymetrix GeneChip® Scanner 3000 7G.
|
| Description |
DR259
DNA methylation data from whole blood samples of Taiwanese patients with proliferative retinopathy of Type-2 Diabetes (T2PDR).
|
| Data processing |
The output data was annotated and the differential methylation of the compared arrays was performed with the tilling analysis software (TAS) of Affymetrix update to 1.0.3 version. It resulted in CHP files and text files.
The differential methylation levels were determined by the MAT (Model-based Analysis of Tiling-array) score which based on T value of ANOVA method, which was performed by the Partek Genomics suite (version 7.18.0723).
|
| |
|
| Submission date |
Oct 25, 2018 |
| Last update date |
Jan 07, 2020 |
| Contact name |
Fuu-Jen Tsai |
| E-mail(s) |
d0704@mail.cmuh.org.tw
|
| Organization name |
China Medical University Hospital
|
| Department |
Department of Medical Research
|
| Lab |
Genetic Center
|
| Street address |
No.2, Yude Rd., North Dist.
|
| City |
Taichung |
| ZIP/Postal code |
40447 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL5082 |
| Series (2) |
| GSE121820 |
DNA methylation profiles in Taiwanese patients of Type-2 Diabetes (T2D) associated to Nephropathy (DN) and Retinopathy (DR) |
| GSE189007 |
Gene-expression profiles of whole blood cells from a Han Chinese population with or without Type-2 Diabetes Mellitus or/and its complications in nephropathy and retinopathy |
|
