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Sample GSM401589 Query DataSets for GSM401589
Status Public on Apr 20, 2010
Title UMARY-4841-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: female
age (y): 42
pmi (hr): 17
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 0.7039928 14376 3.678E-38 21 27 470.9142 985.2538 4185 10191
cg00002426 0.04719945 12951 3.678E-38 24 22 977.3464 89.20226 12335 616
cg00003994 0.0180358 14593 3.678E-38 17 17 1763.234 42.44373 14328 265
cg00005847 0.08107924 14577 3.678E-38 16 25 677.75 103.75 13387 1190
cg00006414 0.02974026 7600 3.678E-38 7 22 631.5786 55.56078 7371 229
cg00007981 0.02455721 9103 3.678E-38 16 15 722 50.25 8877 226
cg00008493 0.9831873 22502 3.678E-38 9 20 74.33334 2254.667 280 22222
cg00008713 0.01913292 23681 3.678E-38 20 11 1580.9 36.2243 23226 455
cg00009407 0.05341491 22946 3.678E-38 20 19 1819.489 131.928 21715 1231
cg00010193 0.6109375 42469 3.678E-38 16 7 2106.5 1963.25 16462 26007
cg00011459 0.9447139 14334 3.678E-38 14 19 129.6217 1202.676 698 13636
cg00012199 0.01204128 17340 3.678E-38 22 13 915.4839 32.19331 17130 210
cg00012386 0.01359974 24974 3.678E-38 15 20 2363.553 57.06195 24633 341
cg00012792 0.02000134 29748 3.678E-38 20 13 2460.122 67.52925 29151 597
cg00013618 0.9145482 19490 3.678E-38 10 22 123.0126 1702.886 1574 17916
cg00014085 0.03133316 14932 3.678E-38 23 17 698.7318 61.92878 14461 471
cg00014837 0.8771554 8773 3.678E-38 34 23 86.26379 473.3361 990 7783
cg00015770 0.0956948 32744 3.678E-38 11 16 2209.174 360.9091 29601 3143
cg00016968 0.8726548 29748 3.678E-38 18 17 330.2189 2021.147 3701 26047
cg00019495 0.02768784 17814 3.678E-38 14 14 1949.938 57.72843 17318 496

Total number of rows: 27578

Table truncated, full table size 1905 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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