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Sample GSM401744 Query DataSets for GSM401744
Status Public on Apr 20, 2010
Title UMARY-1454-FCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: FCTX
Organism Homo sapiens
Characteristics tissue: frontal cortex
gender: female
age (y): 47
pmi (hr): 24
tissuebank: UMARY
prep_hyb_batch: PLATE_Z
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 0.7004255 16350 3.678E-38 11 16 564.4293 598.5 4828 11522
cg00002426 0.196049 8556 3.678E-38 21 20 553.837 93.39725 6859 1697
cg00003994 0.02501651 12012 3.678E-38 17 26 428.3179 30.07442 11709 303
cg00005847 0.1468608 15493 3.678E-38 14 19 734.7012 179.8668 13203 2290
cg00006414 0.02792783 8601 3.678E-38 18 15 432.0422 27.10576 8358 243
cg00007981 0.01348765 10873 3.678E-38 24 19 738.7253 13.67632 10725 148
cg00008493 0.9811462 22654 3.678E-38 13 16 33.83671 761.326 329 22325
cg00008713 0.02340258 26521 3.678E-38 23 18 1027.976 41.49437 25898 623
cg00009407 0.05536858 27533 3.678E-38 19 24 1148.685 111.2666 26003 1530
cg00010193 0.5618106 51396 3.678E-38 18 21 936.9165 925.3671 22465 28931
cg00011459 0.9522178 11285 3.678E-38 30 20 44.00038 658.7277 444 10841
cg00012199 0.00877915 21770 3.678E-38 11 20 1070.365 32.56322 21578 192
cg00012386 0.01896827 26787 3.678E-38 27 21 990.1557 42.33902 26277 510
cg00012792 0.01645938 32222 3.678E-38 17 27 1738.253 50.20488 31690 532
cg00013618 0.9020582 21423 3.678E-38 9 23 155.6667 1292 2008 19415
cg00014085 0.01903427 22018 3.678E-38 24 22 749.3397 33.47636 21597 421
cg00014837 0.8970264 5785 3.678E-38 19 23 38.77126 571.0157 506 5279
cg00015770 0.1033249 34848 3.678E-38 14 14 873.677 110.1116 31237 3611
cg00016968 0.7575669 34260 3.678E-38 18 18 462.6835 1295.184 8230 26030
cg00019495 0.1266741 13265 3.678E-38 18 21 639.4602 149.9066 11572 1693

Total number of rows: 27578

Table truncated, full table size 1903 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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