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Sample GSM401781 Query DataSets for GSM401781
Status Public on Apr 20, 2010
Title UMARY-4789-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: female
age (y): 72
pmi (hr): 19
tissuebank: UMARY
prep_hyb_batch: PLATE_V
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 0.5213764 20156 3.678E-38 16 12 452 711.5 9595 10561
cg00002426 0.136544 14518 3.678E-38 16 21 764 147 12522 1996
cg00003994 0.02835912 14569 3.678E-38 13 20 726.9346 68.78282 14153 416
cg00005847 0.1522143 18755 3.678E-38 21 11 802.8236 94.05191 15885 2870
cg00006414 0.01870488 9042 3.678E-38 17 13 616.283 27.64906 8871 171
cg00007981 0.01894167 13204 3.678E-38 16 8 1488 40 12952 252
cg00008493 0.986465 23838 3.678E-38 15 16 30.46747 1129.62 224 23614
cg00008713 0.0232904 29483 3.678E-38 14 9 811.1379 72.4278 28794 689
cg00009407 0.04549504 32453 3.678E-38 7 13 1251.44 258.9057 30972 1481
cg00010193 0.6214528 49693 3.678E-38 16 17 1985.75 1300.5 18749 30944
cg00011459 0.9521332 18159 3.678E-38 24 14 87.56926 655.2385 774 17385
cg00012199 0.003092204 21244 3.678E-38 7 10 1679.296 14.74061 21178 66
cg00012386 0.01716797 29024 3.678E-38 18 14 2319.074 58.92556 28524 500
cg00012792 0.01662329 42551 3.678E-38 26 13 2152.963 56.87368 41842 709
cg00013618 0.9123071 26470 3.678E-38 21 16 128.7486 727.102 2230 24240
cg00014085 0.02055015 21603 3.678E-38 21 29 1209.8 42.98893 21157 446
cg00014837 0.9017357 10962 3.678E-38 23 9 85.69942 437.6718 987 9975
cg00015770 0.09393132 35575 3.678E-38 19 23 1432.701 119.0668 32224 3351
cg00016968 0.7461725 48366 3.678E-38 18 9 511.7096 782.2958 12202 36164
cg00019495 0.1426605 20964 3.678E-38 16 15 921.75 222 17959 3005

Total number of rows: 27578

Table truncated, full table size 1908 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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