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Sample GSM401979 Query DataSets for GSM401979
Status Public on Apr 20, 2010
Title BLSA-1603-TCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: TCTX
Organism Homo sapiens
Characteristics gender: male
age: 89
pmi: 16
tissuebank: BLSA
prep_hyb_batch: PLATE_Z
tissue: temporal cortex
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: TCTX
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 15, 2009
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 (1)
GSE15745 Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues

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 0.5999638 22033 3.678E-38 18 23 658.7878 822.6009 8754 13279
cg00002426 0.1686063 14164 3.678E-38 23 20 705.8213 194.1269 11759 2405
cg00003994 0.02670553 16713 3.678E-38 18 16 699.8 58.92556 16264 449
cg00005847 0.1837835 18079 3.678E-38 21 15 632.1772 183.0848 14738 3341
cg00006414 0.04469495 10013 3.678E-38 19 25 274.3812 51.61854 9561 452
cg00007981 0.01382958 15591 3.678E-38 9 18 1167.333 37.33333 15374 217
cg00008493 0.988139 23844 3.678E-38 14 14 18.17377 885.7037 184 23660
cg00008713 0.01558831 30564 3.678E-38 15 16 975.9918 41.82822 30086 478
cg00009407 0.05573186 27945 3.678E-38 18 16 618.4827 142.5999 26382 1563
cg00010193 0.5895807 47600 3.678E-38 15 23 989.9346 963.5983 19477 28123
cg00011459 0.9642973 18386 3.678E-38 14 31 63.07365 1137.464 560 17826
cg00012199 0.009062033 21308 3.678E-38 14 21 795.1022 20.31186 21114 194
cg00012386 0.01676252 34501 3.678E-38 13 16 1563.977 77.10332 33921 580
cg00012792 0.01574573 41054 3.678E-38 21 22 1373.027 53.24517 40406 648
cg00013618 0.8973804 24369 3.678E-38 29 16 118.2879 588.6542 2411 21958
cg00014085 0.02988039 23059 3.678E-38 18 21 892.8401 75.18902 22367 692
cg00014837 0.9034009 10956 3.678E-38 17 20 115.447 544.0074 968 9988
cg00015770 0.1345532 35752 3.678E-38 14 14 892.6525 211.9382 30928 4824
cg00016968 0.7425216 39915 3.678E-38 11 15 653.6766 1462.029 10203 29712
cg00019495 0.1028643 19975 3.678E-38 20 25 1152.917 182.9104 17910 2065

Total number of rows: 27578

Table truncated, full table size 1909 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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