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Sample GSM401768 Query DataSets for GSM401768
Status Public on Apr 20, 2010
Title UMARY-4841-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: female
age (y): 42
pmi (hr): 17
tissuebank: UMARY
prep_hyb_batch: PLATE_S
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 0.6123363 5931 3.678E-38 18 24 326.6833 563.3284 2238 3693
cg00002426 0.2434586 8308 3.678E-38 19 22 1131.249 245.4748 6261 2047
cg00003994 0.03015177 14725 3.678E-38 14 21 2817.201 98.35213 14278 447
cg00005847 0.0892259 10648 3.678E-38 26 17 1084.13 98.4503 9689 959
cg00006414 0.03364512 7063 3.678E-38 14 13 954.6572 37.41657 6822 241
cg00007981 0.06898518 3408 3.678E-38 17 19 620.1636 59.66376 3166 242
cg00008493 0.9817865 20544 3.678E-38 7 20 37.79645 4025.322 276 20268
cg00008713 0.04849601 8045 3.678E-38 11 6 737.4968 27.73904 7650 395
cg00009407 0.04513684 23650 3.678E-38 22 22 2933.855 140.0729 22578 1072
cg00010193 0.7002823 40288 3.678E-38 18 24 937.6236 3200.837 12005 28283
cg00011459 0.9104925 6905 3.678E-38 12 15 109.1192 1059.438 527 6378
cg00012199 0.01627169 14711 3.678E-38 21 19 1789.387 32.73269 14470 241
cg00012386 0.03725747 8301 3.678E-38 14 11 1119.29 51.58142 7988 313
cg00012792 0.02185909 37230 3.678E-38 22 14 5346.435 112.7832 36414 816
cg00013618 0.9102699 16093 3.678E-38 26 13 162.9725 1875.851 1353 14740
cg00014085 0.03095294 12629 3.678E-38 18 16 1326.768 39.12658 12235 394
cg00014837 0.828766 6359 3.678E-38 17 19 158.8608 875.0685 1006 5353
cg00015770 0.09031998 34621 3.678E-38 16 21 3628.75 442.25 31485 3136
cg00016968 0.8036113 42046 3.678E-38 15 8 747.4858 2602.128 8177 33869
cg00019495 0.2458944 18107 3.678E-38 21 27 1928.61 714.2272 13630 4477

Total number of rows: 27578

Table truncated, full table size 1895 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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