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Sample GSM401721 Query DataSets for GSM401721
Status Public on Apr 20, 2010
Title UMARY-1134-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 41
pmi (hr): 15
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 0.7054808 15865 3.678E-38 12 18 531.4509 574.1749 4602 11263
cg00002426 0.2496248 7896 3.678E-38 18 22 373.1167 175.1268 5900 1996
cg00003994 0.03333873 12258 3.678E-38 14 12 684.1888 41.42549 11846 412
cg00005847 0.1134337 14587 3.678E-38 15 18 729.67 87.78762 12921 1666
cg00006414 0.04321278 8416 3.678E-38 11 10 673.2748 26.23149 8048 368
cg00007981 0.01776825 12957 3.678E-38 19 16 630.205 29.59463 12725 232
cg00008493 0.9671483 21908 3.678E-38 17 15 47.29445 957.7732 623 21285
cg00008713 0.02618596 28885 3.678E-38 17 12 1056.97 60.87644 28126 759
cg00009407 0.06115654 26929 3.678E-38 13 12 908.5989 131.4639 25276 1653
cg00010193 0.6399919 49060 3.678E-38 15 14 1344.183 1412.606 17598 31462
cg00011459 0.9138985 9714 3.678E-38 16 25 66 703.25 745 8969
cg00012199 0.01002608 22142 3.678E-38 27 18 961.0958 17.70541 21919 223
cg00012386 0.01408234 25890 3.678E-38 21 22 1503.521 38.18813 25524 366
cg00012792 0.01716386 32818 3.678E-38 10 22 1481.211 58.50214 32253 565
cg00013618 0.8979775 19974 3.678E-38 16 18 161 560.5 1948 18026
cg00014085 0.02257282 20500 3.678E-38 16 20 1048.5 49.25 20035 465
cg00014837 0.8849306 5879 3.678E-38 14 25 94.07596 424.6781 588 5291
cg00015770 0.09779986 34716 3.678E-38 21 23 1159.392 162.1359 31311 3405
cg00016968 0.662113 37306 3.678E-38 22 14 586.3019 841.29 12539 24767
cg00019495 0.4002901 12311 3.678E-38 10 21 626.131 413.3097 7343 4968

Total number of rows: 27578

Table truncated, full table size 1900 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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