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Sample GSM401759 Query DataSets for GSM401759
Status Public on Apr 20, 2010
Title BLSA-1603-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 89
pmi (hr): 16
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 0.6265337 23779 3.678E-38 17 20 256.8452 972.8104 8818 14961
cg00002426 0.1520164 15497 3.678E-38 16 24 793.25 188.5 13126 2371
cg00003994 0.05297897 17020 3.678E-38 9 15 1333.667 196 16113 907
cg00005847 0.1531073 17600 3.678E-38 27 14 684.545 91.99114 14890 2710
cg00006414 0.0351463 11281 3.678E-38 19 13 717.6124 42.67133 10881 400
cg00007981 0.007971925 22981 3.678E-38 27 13 1221.288 17.12806 22797 184
cg00008493 0.9822073 27608 3.678E-38 19 24 42.67133 806.1669 393 27215
cg00008713 0.02318901 38539 3.678E-38 21 18 1217.656 65.9018 37643 896
cg00009407 0.05204904 35136 3.678E-38 14 17 1064.234 153.9425 33302 1834
cg00010193 0.6191156 62247 3.678E-38 20 14 1083.151 1305.193 23647 38600
cg00011459 0.9262369 12047 3.678E-38 16 21 70 654.75 796 11251
cg00012199 0.006338645 28455 3.678E-38 17 17 1068.612 13.33946 28274 181
cg00012386 0.01284902 40370 3.678E-38 22 26 1971.254 64.17342 39850 520
cg00012792 0.01535602 51541 3.678E-38 20 18 2567.453 91.00797 50748 793
cg00013618 0.8974662 25316 3.678E-38 16 21 110.75 881 2506 22810
cg00014085 0.0206306 28159 3.678E-38 20 24 857.0848 46.063 27576 583
cg00014837 0.8928393 7916 3.678E-38 18 17 103.709 527.9731 759 7157
cg00015770 0.1180582 44251 3.678E-38 15 21 1054.226 356.8309 39015 5236
cg00016968 0.7497334 51473 3.678E-38 19 11 710.5005 1435.913 12807 38666
cg00019495 0.2818417 16906 3.678E-38 23 17 434.544 178.9054 12113 4793

Total number of rows: 27578

Table truncated, full table size 1910 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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