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Sample GSM401757 Query DataSets for GSM401757
Status Public on Apr 20, 2010
Title BLSA-2093-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 86
pmi (hr): 13
tissuebank: BLSA
prep_hyb_batch: PLATE_Z
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) [email protected]
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 0.691631 20703 3.678E-38 21 21 297.8674 692.8418 6315 14388
cg00002426 0.2536109 14647 3.678E-38 18 23 630.5035 270.1148 10907 3740
cg00003994 0.03360228 20226 3.678E-38 8 21 780.9995 115.2584 19543 683
cg00005847 0.1282038 19408 3.678E-38 28 26 392.5161 123.7834 16907 2501
cg00006414 0.02190561 11130 3.678E-38 17 22 579.9027 41.95866 10884 246
cg00007981 0.01169303 20254 3.678E-38 17 21 1317.211 26.67892 20016 238
cg00008493 0.9834166 28543 3.678E-38 17 16 39.29077 1054.302 375 28168
cg00008713 0.02195242 36388 3.678E-38 22 23 1563.188 45.19855 35587 801
cg00009407 0.05180726 34953 3.678E-38 17 16 1139.19 250.0542 33137 1816
cg00010193 0.6097787 61360 3.678E-38 25 17 849.8 1111.8 23883 37477
cg00011459 0.9379017 13749 3.678E-38 24 19 87.56926 614.2095 760 12989
cg00012199 0.005932882 27374 3.678E-38 21 19 990.2728 17.89387 27211 163
cg00012386 0.01138732 40208 3.678E-38 16 18 1705.5 66.25 39749 459
cg00012792 0.01539755 48674 3.678E-38 19 19 1382.459 71.80712 47923 751
cg00013618 0.9066264 28709 3.678E-38 17 19 184.0845 892.5311 2590 26119
cg00014085 0.02004275 28439 3.678E-38 16 15 1207.25 63.25 27867 572
cg00014837 0.8912246 8891 3.678E-38 20 18 67.08204 489.9225 878 8013
cg00015770 0.1230956 45913 3.678E-38 19 24 1258.804 240.1983 40249 5664
cg00016968 0.6981668 49868 3.678E-38 22 9 520.8494 709.7452 14982 34886
cg00019495 0.3935046 18929 3.678E-38 17 17 739.4911 317.9642 11441 7488

Total number of rows: 27578

Table truncated, full table size 1912 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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