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Sample GSM402028 Query DataSets for GSM402028
Status Public on Apr 20, 2010
Title BLSA-1805-TCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: TCTX
Organism Homo sapiens
Characteristics gender: male
age: 82
pmi: 5.5
tissuebank: BLSA
prep_hyb_batch: PLATE_S
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 0.6298331 19194 3.678E-38 7 20 654.2565 818.671 7042 12152
cg00002426 0.2369396 10160 3.678E-38 23 18 377.6196 172.0244 7729 2431
cg00003994 0.03059155 17650 3.678E-38 18 19 509.3526 43.60492 17107 543
cg00005847 0.1760157 19296 3.678E-38 15 10 730.1865 192.8746 15882 3414
cg00006414 0.06714459 9804 3.678E-38 18 17 271.7647 45.01913 9139 665
cg00007981 0.01350038 18418 3.678E-38 16 16 1049.25 32.75 18168 250
cg00008493 0.9721838 33873 3.678E-38 15 20 101.9886 1102.251 845 33028
cg00008713 0.01384671 41715 3.678E-38 19 17 1163.367 38.77126 41136 579
cg00009407 0.07420769 29560 3.678E-38 15 17 773.3057 256.6497 27359 2201
cg00010193 0.5813664 66629 3.678E-38 12 18 1391.991 1487.543 27835 38794
cg00011459 0.9498339 12239 3.678E-38 16 18 44.5 587.5 519 11720
cg00012199 0.01352396 23192 3.678E-38 19 16 486.5908 24.54748 22877 315
cg00012386 0.01752452 34366 3.678E-38 20 15 1411.406 45.83939 33762 604
cg00012792 0.01063202 59249 3.678E-38 25 19 1433 56.6 58618 631
cg00013618 0.9046786 22770 3.678E-38 16 16 108.5 869.25 2080 20690
cg00014085 0.03664233 21951 3.678E-38 13 19 838.9841 65.45462 21143 808
cg00014837 0.902347 10765 3.678E-38 25 17 78.6 442.2 961 9804
cg00015770 0.09312787 52140 3.678E-38 17 21 1070.31 252.7221 47275 4865
cg00016968 0.771113 41995 3.678E-38 17 10 397.5159 1413.255 9535 32460
cg00019495 0.1887148 12093 3.678E-38 21 19 426.1795 164.9727 9792 2301

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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