|
| Status |
Public on Mar 21, 2016 |
| Title |
t4099_neuron |
| Sample type |
genomic |
| |
|
| Source name |
Brain t4099, neurons from Alzheimer's disease temporal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Neurons, temporal cortex
diagnosis: Alzheimer's disease
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA samples were isolated using Phenol-chloroform extraction protocol. Genomic DNA (500 ng) was then bisulfite-converted using the EpiTect Bisulfite Kit (Qiagen)
|
| Label |
Cy5 and Cy3
|
| Label protocol |
According to manufacturers instructions.
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.
|
| Scan protocol |
Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).
|
| Description |
Neurons from Alzheimer's disease temporal cortex
|
| Data processing |
Data was extracted using GenomeStudio v2011.1. Background correction, normalization to Illumina internal control probes, and quantile normalization were performed. All probes mapping to the X or Y chromosome were removed, along with probes that queried CpGs overlapping the positions of known common DNA variants as reported in dbSNP build 138 (allele frequency>1 percent). As recommended by Illumina, fractional methylation (AVG_Beta) values with a detection p-value>0.05 were excluded from the analysis and replaced by missing values. In each tissue, probes with more than 20 percent missing values were excluded.
|
| |
|
| Submission date |
Mar 11, 2016 |
| Last update date |
Mar 21, 2016 |
| Contact name |
Benjamin Tycko |
| E-mail(s) |
bejamintycko@hackensackmeridian.org
|
| Phone |
5519963595
|
| Organization name |
HUMC
|
| Department |
Epigenetics
|
| Street address |
40 prospect avenue
|
| City |
hackensack |
| State/province |
NJ |
| ZIP/Postal code |
07601 |
| Country |
USA |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE79144 |
Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation: Methylation array data for the identification of mQTL |
| GSE79262 |
Mechanisms and disease associations of haplotype-dependent allele specific DNA methylation |
|
