NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM401892 Query DataSets for GSM401892
Status Public on Apr 20, 2010
Title UMARY-4915-PONS-CpG
Sample type genomic
 
Source name Human Brain Tissue: PONS
Organism Homo sapiens
Characteristics gender: male
age: 49
pmi: 5
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 0.7130498 16314 3.678E-38 18 22 278.1287 363.4529 4610 11704
cg00002426 0.3160104 16102 3.678E-38 13 10 602.6818 133.6828 10982 5120
cg00003994 0.02399283 26658 3.678E-38 20 18 975.1492 64.17515 26016 642
cg00005847 0.6580733 33647 3.678E-38 21 16 363.9874 694.5875 11439 22208
cg00006414 0.0816879 12460 3.678E-38 17 17 805.9459 84.4024 11434 1026
cg00007981 0.0185456 14944 3.678E-38 18 16 773.8105 42.1907 14665 279
cg00008493 0.9805356 37353 3.678E-38 12 17 83.13844 1315.781 629 36724
cg00008713 0.02009932 38160 3.678E-38 21 28 1084.106 60.00992 37391 769
cg00009407 0.04891846 40028 3.678E-38 12 26 772.206 213.9083 38065 1963
cg00010193 0.5917072 69044 3.678E-38 19 14 1431.095 1337.494 28131 40913
cg00011459 0.946778 15946 3.678E-38 17 18 95.3165 734.6404 754 15192
cg00012199 0.0157871 24287 3.678E-38 20 21 840.538 38.46037 23902 385
cg00012386 0.01455162 38796 3.678E-38 15 24 1730.449 93.2098 38230 566
cg00012792 0.01165451 55844 3.678E-38 12 20 2029.964 72.45746 55192 652
cg00013618 0.9128577 31733 3.678E-38 9 14 58 1777.333 2674 29059
cg00014085 0.0340417 24840 3.678E-38 17 14 599.063 81.49197 23991 849
cg00014837 0.9181663 12792 3.678E-38 22 22 108.9456 525.9662 955 11837
cg00015770 0.08742636 54220 3.678E-38 15 25 1325.851 181.2556 49471 4749
cg00016968 0.7874763 54181 3.678E-38 10 20 664.7108 2387.52 11436 42745
cg00019495 0.2559842 24632 3.678E-38 14 21 2586.822 640.6252 18301 6331

Total number of rows: 27578

Table truncated, full table size 1914 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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