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Status |
Public on Mar 21, 2016 |
Title |
t4053_neuron |
Sample type |
genomic |
|
|
Source name |
Brain t4053, 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.
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|
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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 |
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