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Sample GSM401754 Query DataSets for GSM401754
Status Public on Apr 20, 2010
Title BLSA-2020-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 82
pmi (hr): 14.5
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) 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 0.7161912 22091 3.678E-38 16 19 655.25 797 6198 15893
cg00002426 0.1735715 12886 3.678E-38 15 9 1011.623 86.75483 10632 2254
cg00003994 0.04912664 12724 3.678E-38 10 23 1120.711 109.731 12094 630
cg00005847 0.1386538 17505 3.678E-38 16 24 674 162.75 15064 2441
cg00006414 0.03197442 11159 3.678E-38 19 10 371.4241 22.94157 10799 360
cg00007981 0.01324777 19224 3.678E-38 20 14 984.3171 36.67152 18968 256
cg00008493 0.9817293 25077 3.678E-38 21 17 46.91685 726.0109 360 24717
cg00008713 0.01977313 35251 3.678E-38 18 19 1234.608 47.14045 34552 699
cg00009407 0.05010163 29420 3.678E-38 21 18 1019.514 93.83369 27941 1479
cg00010193 0.6135286 54732 3.678E-38 17 14 1207.342 1563.627 21091 33641
cg00011459 0.935644 12191 3.678E-38 19 28 64.69524 810.067 691 11500
cg00012199 0.00622654 22545 3.678E-38 26 17 882.5226 13.53201 22404 141
cg00012386 0.01733833 34044 3.678E-38 24 18 1588.29 66.95272 33452 592
cg00012792 0.01256186 44559 3.678E-38 17 23 2388.976 49.96234 43998 561
cg00013618 0.9007735 23301 3.678E-38 18 14 121.8581 1244.036 2222 21079
cg00014085 0.020531 24156 3.678E-38 19 18 946.1105 50.70088 23658 498
cg00014837 0.9036102 8376 3.678E-38 17 24 73.97337 458.8774 717 7659
cg00015770 0.1010201 41466 3.678E-38 20 19 1477.146 268.3282 37267 4199
cg00016968 0.7464418 42127 3.678E-38 12 10 628.4457 1681.821 10607 31520
cg00019495 0.2651568 15619 3.678E-38 23 16 505.2304 238.9575 11451 4168

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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