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Sample GSM1300399 Query DataSets for GSM1300399
Status Public on Jun 01, 2014
Title 7973201148_R04C02 (batch2)
Sample type genomic
 
Source name 7973201148_R04C02
Organism Homo sapiens
Characteristics diagnosis: Control
gender: UNKNOWN
race: White
age: 70
tau_a1: H1
tau_a2: H2
batch: 2
tissue: Peripheral Blood
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted and purified with standard methods
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Data processing BeadStudio software
Raw data was processed using the Illumina GenomeStudio software (version 2010.3). Background correction and color normalization were performed using the R package minfi version 1.2.0 and normalization using Subset-quantile Within Array Normalization (SWAN). Probes were excluded from further analysis if >95% samples had detection p-value >0.01.
Raw data (Unmethylated and methylated signal intensities) linked as supplementary files on Series record.
 
Submission date Jan 02, 2014
Last update date Jun 01, 2014
Contact name Giovanni Coppola
E-mail(s) gcoppola@ucla.edu
Phone 310-794-4172
Organization name UCLA
Department Psychiatry and Neurology
Lab Neurogenetics
Street address 1524 Gonda, 695 Charles Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL13534
Series (1)
GSE53740 An Epigenetic Signature in Peripheral Blood Associated with Neurodegenerative Tauopathy and the Risk-Associated Haplotype on 17q21.31

Data table header descriptions
ID_REF
VALUE quantile-normalized beta values
DetectionPval

Data table
ID_REF VALUE DetectionPval
cg00050873 0.315926407145502 0.797835797000209
cg00212031 0.363961347658693 0.97213244216116
cg00213748 0.510840382410202 0.976521169099033
cg00214611 0.844876108345118 0.804675994475076
cg00455876 0.139452169279396 0.000958957334972532
cg01707559 0.267327474370888 0
cg02004872 0.0759883486933418 1.9490298264202e-11
cg02011394 0.540589256217722 0.976521169099033
cg02050847 0.153522087535172 0.649759227130425
cg02233190 0.248304730819193 0.0196821409780198
cg02494853 0.00915250745150512 0
cg02839557 0.540589256217722 0.95699995898609
cg02842889 0.654057647530587 0.905256010129735
cg03052502 0.291561762801601 0.921675264252192
cg03155755 0.31226727765171 0.874233601026542
cg03244189 0.179585984147652 0
cg03443143 0.572458001824585 0.599247991819454
cg03683899 0.212771348134838 0.516812700314893
cg03695421 0.0846056925362552 0.0246777221041874
cg03706273 0.0314176900635643 0

Total number of rows: 485577

Table truncated, full table size 15378 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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