|
| Status |
Public on May 15, 2016 |
| Title |
DNA-methylations on Whole blood of DCCT/EDIC participant ID 1535 |
| Sample type |
genomic |
| |
|
| Source name |
Case_blood draw
|
| Organism |
Homo sapiens |
| Characteristics |
participant id: 1535
sample group: Case
gender: F
age: 49
cell type: whole blood
collection time: EDIC baseline (1993-94)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA extraction and purification method uses sodium dodecylsulfate cell lysis followed by salt precipitation method for protein removal using commercial uregene® reagents (Gentra System, Inc., Minneapolis, MN) in the Molecular Diagnostics Section of the EDIC Central Biochemistry Laboratory.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were scanned by Illumina iScan machine using standard recommended Illumina scanner setting
|
| Description |
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1535
|
| Data processing |
Bioconductor R pachage "Minfi" was used to process data including background substraction, control normalization and Subset-quantile Within Array (SWAN) normalization.
GEO.WB.processed.data.txt: Average beta after data processing
GEO.WB.signal.intensities.data.txt: unmethylated and methylated signal intensities
|
| |
|
| Submission date |
Dec 18, 2015 |
| Last update date |
May 15, 2016 |
| Contact name |
Nancy Chen |
| E-mail(s) |
zhuchen@coh.org
|
| Organization name |
City of Hope
|
| Department |
Diabetes
|
| Street address |
1500 Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL16304 |
| Series (2) |
| GSE76169 |
DNA-methylation profiling of Whole blood genomic DNAs collected from participants of Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study |
| GSE76171 |
DNA-methylation profiling of Whole blood genomic DNAs collected at EDIC baseline and monocytes at EDIC years 16/17 yrs from participants of DCCT/EDIC study |
|
