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Sample GSM401726 Query DataSets for GSM401726
Status Public on Apr 20, 2010
Title UMARY-1846-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: female
age (y): 20
pmi (hr): 9
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 0.6409544 11425 3.678E-38 24 24 173.9138 322.1079 4038 7387
cg00002426 0.1629883 8962 3.678E-38 27 19 338.7122 117.0097 7485 1477
cg00003994 0.02321066 11231 3.678E-38 24 21 408.2483 36.12997 10968 263
cg00005847 0.1359051 13976 3.678E-38 23 15 521.7031 70.06084 12063 1913
cg00006414 0.02213431 10517 3.678E-38 14 13 599.1997 25.12256 10282 235
cg00007981 0.01782832 14147 3.678E-38 13 21 994.3001 51.86447 13893 254
cg00008493 0.9801614 25053 3.678E-38 16 23 41.75 1033 399 24654
cg00008713 0.0257311 32351 3.678E-38 20 18 956.1426 91.45518 31516 835
cg00009407 0.05315195 26804 3.678E-38 20 18 997.7335 93.91486 25374 1430
cg00010193 0.5950062 50923 3.678E-38 23 10 1180.192 1026.308 20564 30359
cg00011459 0.9468192 7854 3.678E-38 25 18 35 267.4 323 7531
cg00012199 0.006490697 23010 3.678E-38 22 17 531.7226 11.93924 22860 150
cg00012386 0.0141133 30722 3.678E-38 13 21 996.7963 51.30977 30287 435
cg00012792 0.01459103 37800 3.678E-38 17 24 1377.845 51.41755 37247 553
cg00013618 0.9021682 20793 3.678E-38 21 29 133.1129 763.9808 1944 18849
cg00014085 0.0293884 22562 3.678E-38 25 21 690.2 39.2 21896 666
cg00014837 0.8905693 5785 3.678E-38 14 11 59.332 365.3461 544 5241
cg00015770 0.09604971 33695 3.678E-38 14 9 539.8677 215.1453 30449 3246
cg00016968 0.7224516 41799 3.678E-38 19 14 458.1432 1132.625 11529 30270
cg00019495 0.3456931 12171 3.678E-38 16 31 397.75 294.25 7929 4242

Total number of rows: 27578

Table truncated, full table size 1902 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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