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Sample GSM401786 Query DataSets for GSM401786
Status Public on Apr 20, 2010
Title UMARY-1710-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: female
age (y): 26
pmi (hr): 12
tissuebank: UMARY
prep_hyb_batch: PLATE_V
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 0.5762801 16949 3.678E-38 11 27 391.9648 889.157 7124 9825
cg00002426 0.2049752 12804 3.678E-38 18 15 646.0599 299.5776 10159 2645
cg00003994 0.01867733 13660 3.678E-38 17 15 723.9688 35.89527 13403 257
cg00005847 0.135393 17087 3.678E-38 29 19 801.8325 156.7269 14760 2327
cg00006414 0.025267 7578 3.678E-38 15 25 492.1271 15.49193 7384 194
cg00007981 0.01949642 10107 3.678E-38 20 22 967.5466 21.01904 9908 199
cg00008493 0.9873086 21253 3.678E-38 18 19 19.56329 729.7342 171 21082
cg00008713 0.00900539 29771 3.678E-38 15 10 1694.559 26.85268 29502 269
cg00009407 0.0319711 29239 3.678E-38 17 14 1346.558 114.9619 28301 938
cg00010193 0.6593603 40048 3.678E-38 22 18 1092.654 1640.366 13576 26472
cg00011459 0.9345627 15029 3.678E-38 26 23 104.1377 834.278 890 14139
cg00012199 0.007334289 18034 3.678E-38 12 13 1464.16 10.96966 17901 133
cg00012386 0.01214729 28713 3.678E-38 19 24 1208.792 54.60094 28363 350
cg00012792 0.01117198 41701 3.678E-38 20 24 1933.752 55.67809 41234 467
cg00013618 0.9083451 22572 3.678E-38 25 13 134.2 495.6 1978 20594
cg00014085 0.01572357 20506 3.678E-38 20 21 647.3417 33.54102 20182 324
cg00014837 0.9082013 9301 3.678E-38 19 23 91.30746 461.5844 763 8538
cg00015770 0.07165976 35122 3.678E-38 16 16 1142.75 248.5 32598 2524
cg00016968 0.6990221 39986 3.678E-38 21 10 615.1563 1850.27 11965 28021
cg00019495 0.2498444 15962 3.678E-38 12 10 660.7774 687.3355 11949 4013

Total number of rows: 27578

Table truncated, full table size 1907 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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