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Sample GSM401718 Query DataSets for GSM401718
Status Public on Apr 20, 2010
Title UMARY-1260-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 42
pmi (hr): 8
tissuebank: UMARY
prep_hyb_batch: PLATE_Y
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

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 0.6577097 16684 3.678E-38 27 23 280.0149 492.8647 5645 11039
cg00002426 0.1898354 9561 3.678E-38 10 17 1106.165 279.8616 7727 1834
cg00003994 0.0203675 13451 3.678E-38 17 15 581.843 34.68259 13175 276
cg00005847 0.1077619 14497 3.678E-38 8 16 589.02 178.898 12924 1573
cg00006414 0.02468184 10272 3.678E-38 17 23 414.2509 20.61553 10016 256
cg00007981 0.01095815 14501 3.678E-38 22 13 894.377 16.41645 14341 160
cg00008493 0.9786048 22148 3.678E-38 23 19 30.86013 1185.404 376 21772
cg00008713 0.02961022 33098 3.678E-38 19 12 792.1725 89.93097 32115 983
cg00009407 0.06574249 25941 3.678E-38 10 11 421.5316 142.935 24229 1712
cg00010193 0.6459301 47272 3.678E-38 15 21 901.8887 1265.175 16673 30599
cg00011459 0.9444329 9510 3.678E-38 18 11 53.74012 497.8032 434 9076
cg00012199 0.007647655 21606 3.678E-38 14 15 1623.612 19.77733 21440 166
cg00012386 0.02043408 35331 3.678E-38 18 17 1788.745 43.13351 34607 724
cg00012792 0.01197713 44151 3.678E-38 14 20 3889.987 57.99569 43621 530
cg00013618 0.9055973 21446 3.678E-38 18 18 102.7662 836.743 1934 19512
cg00014085 0.02237236 22249 3.678E-38 25 19 623.4 39.2 21749 500
cg00014837 0.903608 7328 3.678E-38 13 20 88.47468 637.3505 616 6712
cg00015770 0.1333527 37852 3.678E-38 14 16 708.2423 293.4529 32791 5061
cg00016968 0.7267882 36487 3.678E-38 19 13 426.4839 1667.164 9896 26591
cg00019495 0.1259566 12706 3.678E-38 27 16 382.0134 83.90824 11093 1613

Total number of rows: 27578

Table truncated, full table size 1903 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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