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Sample GSM401722 Query DataSets for GSM401722
Status Public on Apr 20, 2010
Title UMARY-1541-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): 19
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 0.5845485 13478 3.678E-38 20 22 289.1236 338.9879 5541 7937
cg00002426 0.1813583 7807 3.678E-38 21 21 415.2686 127.8757 6373 1434
cg00003994 0.01960159 12450 3.678E-38 16 10 473.25 26.5 12204 246
cg00005847 0.1235534 14590 3.678E-38 14 22 767.0397 137.9068 12775 1815
cg00006414 0.0407642 9688 3.678E-38 18 17 812.23 28.28427 9289 399
cg00007981 0.01179961 14731 3.678E-38 19 14 657.5055 28.44755 14556 175
cg00008493 0.9816499 24423 3.678E-38 15 10 44.66841 660.4728 350 24073
cg00008713 0.02654926 29995 3.678E-38 24 15 889.9813 48.9898 29196 799
cg00009407 0.05752449 27975 3.678E-38 20 25 640.8571 158.7608 26360 1615
cg00010193 0.6254674 49650 3.678E-38 27 14 1116.595 716.6841 18533 31117
cg00011459 0.9327335 9013 3.678E-38 22 25 56.92459 479.4884 513 8500
cg00012199 0.009476286 21744 3.678E-38 21 23 887.7104 17.45743 21537 207
cg00012386 0.01777197 28203 3.678E-38 22 22 829.3508 39.65533 27700 503
cg00012792 0.01409566 31470 3.678E-38 15 17 1330.499 37.18064 31025 445
cg00013618 0.9005538 20484 3.678E-38 16 21 142.75 628 1947 18537
cg00014085 0.02523439 19952 3.678E-38 16 16 708.5 32 19446 506
cg00014837 0.8926292 6168 3.678E-38 20 11 48.52267 256.7006 573 5595
cg00015770 0.07381173 35477 3.678E-38 16 17 1169.5 176.75 32851 2626
cg00016968 0.7012889 39547 3.678E-38 20 12 484.3323 1016.516 11743 27804
cg00019495 0.1915123 11022 3.678E-38 17 16 774.1737 157.8907 8892 2130

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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