|
| Status |
Public on Apr 20, 2010 |
| Title |
JHU-705-FCTX-CpG |
| Sample type |
genomic |
| |
|
| Source name |
Human Brain Tissue: FCTX
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: frontal cortex
gender: male
age (y): 73
pmi (hr): 9
tissuebank: JHU
prep_hyb_batch: PLATE_W
tissue: FCTX
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA for the Infinium methylation assay was extracted using phenol-chloroform and ethanol precipitation. DNA concentration was determined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE), and DNA extraction was repeated using a new tissue aliquot for samples with DNA concentration less than 50ng/ul, or with a 260/280 ratio less than 1.7.
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
1ug of genomic DNA underwent bisulfite conversion using the WZ-96 DNA Methylation Kit according to the manufacturer’s protocol (Zymo Research Corp, Orange, CA). Incubation conditions used during conversion were as follows: (95°C for 30 seconds, 50°C for 1 hour) for 16 cycles, hold overnight at 4°C. Unmethylated cytosines were chemically deaminated to uracil in the presence of bisulfite, while methylated cytosines were refractory to the effects of bisulfite and remained as cytosines. Methylation was then detected as a C/T nucleotide polymorphism at each CpG site. After bisulfite conversion, each sample was whole-genome amplified, fragmented, and hybridized to the BeadChip. DNA molecules anneal to locus-specific DNA oligomers.
|
| |
|
| Hybridization protocol |
Two bead types correspond to each CpG locus, one to the methylated (C) state, and the other to the unmethylated (T) state. After extension, the BeadChip was fluorescently stained.
|
| Scan protocol |
Illumina Beadstation BeadArray laser confocal scanner to measure the intensities of unmethylated and methylated bead types for each locus.
|
| Description |
Human Brain Tissue: FCTX
|
| Data processing |
Beadstudio Methylation Module v3.2.0, no normalization (analysis performed on the non-normalized data).
|
| |
|
| Submission date |
May 11, 2009 |
| Last update date |
May 10, 2012 |
| Contact name |
J Raphael Gibbs |
| E-mail(s) |
gibbsr@mail.nih.gov
|
| Organization name |
National Institutue on Aging, NIH
|
| Department |
Computational Biology Core
|
| Lab |
Laboratory of Neurogenetics
|
| Street address |
35 Convent Drive, Bldg 35/1A1015, MSC3707
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE15745 |
Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues |
| GSE36194 |
North American Brain Expression Consortium: DNA Methylation |
|
