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Sample GSM401596 Query DataSets for GSM401596
Status Public on Apr 20, 2010
Title UMARY-1849-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: male
age (y): 48
pmi (hr): 21
tissuebank: UMARY
prep_hyb_batch: PLATE_Y
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 0.485079 10154 3.678E-38 25 20 492.2 626.4 5180 4974
cg00002426 0.05567475 9222 3.678E-38 19 12 1297.575 73.41303 8703 519
cg00003994 0.01755241 10155 3.678E-38 26 22 1039.416 20.59219 9975 180
cg00005847 0.09697825 16182 3.678E-38 12 15 728.0387 157.9053 14603 1579
cg00006414 0.02934238 6682 3.678E-38 16 9 414.75 33.5 6483 199
cg00007981 0.03837403 6493 3.678E-38 21 17 650.7258 40.80674 6240 253
cg00008493 0.9759176 19707 3.678E-38 16 17 50.5 1916 377 19330
cg00008713 0.02216805 21643 3.678E-38 16 21 2923.5 58.75 21161 482
cg00009407 0.0550367 25919 3.678E-38 25 18 1796.6 177 24487 1432
cg00010193 0.615189 41983 3.678E-38 19 15 1231.733 1937.186 16094 25889
cg00011459 0.9481971 8220 3.678E-38 20 17 29.06888 997.0627 331 7889
cg00012199 0.0105129 15595 3.678E-38 30 13 1134.881 14.97108 15430 165
cg00012386 0.009172789 23993 3.678E-38 14 12 3264.596 24.58803 23772 221
cg00012792 0.01861494 22946 3.678E-38 14 17 3410.521 70.82423 22517 429
cg00013618 0.9111773 17677 3.678E-38 17 18 129.9991 1500.81 1479 16198
cg00014085 0.03030674 16233 3.678E-38 23 19 1065.3 64.43095 15738 495
cg00014837 0.8539791 5454 3.678E-38 15 16 110.2509 620.9683 711 4743
cg00015770 0.09194957 30830 3.678E-38 16 16 2492 244.5 27986 2844
cg00016968 0.9008939 26750 3.678E-38 20 12 271.0114 1797.575 2561 24189
cg00019495 0.03330592 12060 3.678E-38 20 16 1219.328 57.46695 11655 405

Total number of rows: 27578

Table truncated, full table size 1898 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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