NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM401701 Query DataSets for GSM401701
Status Public on Apr 20, 2010
Title JHU-994-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: male
age (y): 49
pmi (hr): 12
tissuebank: JHU
prep_hyb_batch: PLATE_W
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) [email protected]
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 0.6915202 18556 3.678E-38 18 22 367.2241 603.1621 5655 12901
cg00002426 0.2256129 11566 3.678E-38 13 15 639.8467 175.0079 8934 2632
cg00003994 0.03616219 12897 3.678E-38 11 15 816.1912 50.35239 12427 470
cg00005847 0.1168831 14838 3.678E-38 18 26 702.157 150.8494 13092 1746
cg00006414 0.02323694 9755 3.678E-38 17 11 681.7676 20.61553 9526 229
cg00007981 0.01273774 17093 3.678E-38 23 19 1059.879 38.57516 16874 219
cg00008493 0.9836969 26030 3.678E-38 12 16 54.84827 1227.447 326 25704
cg00008713 0.02022899 36234 3.678E-38 22 21 1121.009 44.77215 35499 735
cg00009407 0.05015648 35688 3.678E-38 18 16 775.6962 159.3347 33893 1795
cg00010193 0.6775954 55777 3.678E-38 16 13 1546 1857 17915 37862
cg00011459 0.9423686 10311 3.678E-38 21 19 47.78972 625.4125 500 9811
cg00012199 0.006808279 25604 3.678E-38 18 20 1068.91 14.61354 25429 175
cg00012386 0.01065278 38106 3.678E-38 20 22 1127.873 61.49187 37699 407
cg00012792 0.01575368 48714 3.678E-38 25 19 1953.2 84.2 47945 769
cg00013618 0.9111385 23476 3.678E-38 20 14 77.59156 768.0894 1995 21481
cg00014085 0.02085894 28377 3.678E-38 20 16 1035.747 78.26238 27783 594
cg00014837 0.9030876 6669 3.678E-38 20 17 67.30565 432.4555 556 6113
cg00015770 0.1129166 39655 3.678E-38 24 14 1029.194 190.4478 35166 4489
cg00016968 0.7200249 48065 3.678E-38 21 19 777.7286 1334.839 13385 34680
cg00019495 0.2639471 16839 3.678E-38 13 22 690.6017 283.7292 12368 4471

Total number of rows: 27578

Table truncated, full table size 1907 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap