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Sample GSM401895 Query DataSets for GSM401895
Status Public on Apr 20, 2010
Title UMARY-4549-PONS-CpG
Sample type genomic
 
Source name Human Brain Tissue: PONS
Organism Homo sapiens
Characteristics gender: male
age: 58
pmi: 17
tissuebank: UMARY
prep_hyb_batch: PLATE_S
tissue: pons
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: PONS
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 15, 2009
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 (1)
GSE15745 Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues

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 0.8027506 21132 3.678E-38 17 21 300.0166 900.5348 4088 17044
cg00002426 0.3846404 12205 3.678E-38 17 14 393.8779 374.475 7472 4733
cg00003994 0.02610313 17101 3.678E-38 12 21 396.6396 49.65212 16652 449
cg00005847 0.3618365 22225 3.678E-38 15 24 343.1463 423.188 14147 8078
cg00006414 0.03722575 9517 3.678E-38 18 18 489.0822 43.84062 9159 358
cg00007981 0.01325669 16948 3.678E-38 12 15 883.0573 26.55811 16722 226
cg00008493 0.9822904 28585 3.678E-38 18 15 36.53385 513.8309 408 28177
cg00008713 0.01874264 30472 3.678E-38 14 11 1399.647 48.37429 29899 573
cg00009407 0.04409212 34464 3.678E-38 16 26 1136.75 146.75 32940 1524
cg00010193 0.6257882 55251 3.678E-38 16 19 1058.25 944.5 20613 34638
cg00011459 0.9613676 17010 3.678E-38 26 20 65.69891 619.727 561 16449
cg00012199 0.00809562 26087 3.678E-38 23 18 681.2166 18.55778 25875 212
cg00012386 0.01457653 31732 3.678E-38 11 23 1696.906 93.46851 31268 464
cg00012792 0.00935883 44350 3.678E-38 14 22 1719.826 42.7618 43934 416
cg00013618 0.9069558 28768 3.678E-38 18 11 126.5721 292.2708 2586 26182
cg00014085 0.02757777 28510 3.678E-38 16 15 1045.25 97.5 27721 789
cg00014837 0.9277689 10491 3.678E-38 20 14 65.29318 413.2254 665 9826
cg00015770 0.1174738 42003 3.678E-38 10 16 1285.782 180.2498 37057 4946
cg00016968 0.7574515 45025 3.678E-38 16 24 519 1360.75 10845 34180
cg00019495 0.1647027 18485 3.678E-38 13 15 860.8947 299.2607 15424 3061

Total number of rows: 27578

Table truncated, full table size 1908 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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