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Sample GSM401634 Query DataSets for GSM401634
Status Public on Apr 20, 2010
Title UMARY-4640-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: female
age (y): 47
pmi (hr): 5
tissuebank: UMARY
prep_hyb_batch: PLATE_S
tissue: cerebellum
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: CRBLM
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 0.2418605 115 0.9999939 17 13 8.731282 3.638034 63 52
cg00002426 0.2397959 96 0.9999997 13 16 4.714952 5.269652 49 47
cg00003994 0.2623762 102 0.9999992 18 17 7.542472 8.956686 49 53
cg00005847 0.4121094 412 1.254726E-07 14 23 10.95771 17.37198 201 211
cg00006414 0.3674912 466 2.797032E-12 16 19 15.75 16.5 258 208
cg00007981 0.3622047 154 0.9991057 22 22 5.330018 7.035624 62 92
cg00008493 0.7162921 968 3.678E-38 13 19 11.37135 84.31443 203 765
cg00008713 0.2782071 547 1.172422E-21 18 19 31.5841 8.956686 367 180
cg00009407 0.3244207 461 8.52996E-12 19 8 22.25333 7.341303 279 182
cg00010193 0.4340796 704 3.678E-38 24 8 30.82275 14.69694 355 349
cg00011459 0.2739726 119 0.9999892 11 15 6.934761 9.045341 59 60
cg00012199 0.267341 592 4.039069E-28 20 7 27.28003 10.28591 407 185
cg00012386 0.2891986 187 0.9804978 18 21 13.90643 11.07801 104 83
cg00012792 0.1721068 237 0.6770144 16 14 28.25 8.75 179 58
cg00013618 0.470377 457 2.043893E-11 16 25 10.75 18 195 262
cg00014085 0.3301282 524 1.061949E-18 9 20 34 14.33333 318 206
cg00014837 0.3055556 116 0.999993 16 13 6.5 12.5 50 66
cg00015770 0.2384824 638 1.178379E-35 19 15 41.98308 8.029551 462 176
cg00016968 0.4592445 403 5.630823E-07 21 15 5.019011 14.83882 172 231
cg00019495 0.3125 108 0.9999979 8 13 7.424621 12.72792 43 65

Total number of rows: 27578

Table truncated, full table size 1780 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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