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Sample GSM401548 Query DataSets for GSM401548
Status Public on Apr 20, 2010
Title UMARY-1498-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: male
age (y): 48
pmi (hr): 20
tissuebank: UMARY
prep_hyb_batch: PLATE_X
tissue: cerebellum
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: CRBLM
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

Data table header descriptions
ID_REF
VALUE Illumina Average Beta
Intensity Illumina Intensity
Detection_Pval Illumina Detection p-value
Avg_NBEADS_A Illumina Average Number Beads A
Avg_NBEADS_B Illumina Average Number Beads B
BEAD_STDERR_A Illumina Beads A Standard Error
BEAD_STDERR_B Illumina Beads B Standard Error
Signal_A Illumina Signal A
Signal_B Illumina Signal B

Data table
ID_REF VALUE Intensity Detection_Pval Avg_NBEADS_A Avg_NBEADS_B BEAD_STDERR_A BEAD_STDERR_B Signal_A Signal_B
cg00000292 0.6215841 13586 3.678E-38 11 23 434.1763 463.4229 5079 8507
cg00002426 0.03854119 8592 3.678E-38 29 11 380.1183 32.31099 8257 335
cg00003994 0.02797572 7478 3.678E-38 14 23 491.7607 33.14039 7266 212
cg00005847 0.08885857 10895 3.678E-38 16 14 209.75 49.5 9918 977
cg00006414 0.02536501 7982 3.678E-38 23 18 279.6178 16.26412 7777 205
cg00007981 0.01977127 10218 3.678E-38 17 19 635.6859 26.43638 10014 204
cg00008493 0.9876296 22858 3.678E-38 11 16 22.61335 530.66 184 22674
cg00008713 0.01477721 30826 3.678E-38 17 16 773.6887 30.07442 30369 457
cg00009407 0.04813387 25059 3.678E-38 18 27 648.6526 118.5582 23848 1211
cg00010193 0.6416824 49518 3.678E-38 18 15 959.5439 868.5628 17679 31839
cg00011459 0.9340477 7739 3.678E-38 18 18 56.33284 317.2552 417 7322
cg00012199 0.009313221 17402 3.678E-38 14 20 388.8651 22.71721 17239 163
cg00012386 0.01003316 23422 3.678E-38 21 17 1033.48 22.04001 23186 236
cg00012792 0.00950253 37048 3.678E-38 8 25 1955.15 47.0226 36695 353
cg00013618 0.9180604 22441 3.678E-38 15 20 91.14421 487.4795 1747 20694
cg00014085 0.02742658 19990 3.678E-38 25 15 405.8 48 19439 551
cg00014837 0.8861735 4442 3.678E-38 22 16 38.80253 169.7078 417 4025
cg00015770 0.07035489 33629 3.678E-38 20 19 749.0828 99.05781 31256 2373
cg00016968 0.9054796 37257 3.678E-38 23 13 178.0713 1377.655 3431 33826
cg00019495 0.02634921 9350 3.678E-38 14 15 286.5041 33.94218 9101 249

Total number of rows: 27578

Table truncated, full table size 1895 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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