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Sample GSM401545 Query DataSets for GSM401545
Status Public on Apr 20, 2010
Title UMARY-5086-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: female
age (y): 47
pmi (hr): 20
tissuebank: UMARY
prep_hyb_batch: PLATE_X
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 0.6737241 24177 3.678E-38 10 25 590.7134 1037.227 7821 16356
cg00002426 0.04518021 17629 3.678E-38 32 21 633.7444 45.96194 16828 801
cg00003994 0.01093804 17362 3.678E-38 13 13 1111.896 27.73501 17171 191
cg00005847 0.0992033 20736 3.678E-38 24 17 589.1023 99.20434 18669 2067
cg00006414 0.0306929 11792 3.678E-38 19 17 498.0616 27.52989 11427 365
cg00007981 0.008576814 21120 3.678E-38 16 19 615.5 43.5 20938 182
cg00008493 0.9831228 31244 3.678E-38 12 20 36.37307 950.6072 429 30815
cg00008713 0.02421261 36286 3.678E-38 25 24 809 65.4 35405 881
cg00009407 0.0605742 36995 3.678E-38 13 26 1343.484 178.0588 34748 2247
cg00010193 0.562641 64195 3.678E-38 17 22 935.7025 1064.004 28020 36175
cg00011459 0.9465466 18215 3.678E-38 19 20 78.00135 895.1802 879 17336
cg00012199 0.008895149 26881 3.678E-38 13 17 1092.759 27.18031 26641 240
cg00012386 0.0148441 38097 3.678E-38 22 15 1321.205 58.417 37530 567
cg00012792 0.01534913 50196 3.678E-38 20 29 2279.671 75.8027 49424 772
cg00013618 0.9099266 29598 3.678E-38 16 25 138.5 741.75 2575 27023
cg00014085 0.02684733 27724 3.678E-38 28 15 579.7975 39.87525 26977 747
cg00014837 0.8958766 12414 3.678E-38 17 11 113.0216 254.6624 1203 11211
cg00015770 0.08982203 42885 3.678E-38 13 25 1014.547 158.3669 39024 3861
cg00016968 0.8785896 47120 3.678E-38 14 27 384.5889 2074.482 5633 41487
cg00019495 0.03228314 19198 3.678E-38 20 22 665.9011 66.18761 18575 623

Total number of rows: 27578

Table truncated, full table size 1912 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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