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Sample GSM401588 Query DataSets for GSM401588
Status Public on Apr 20, 2010
Title UMARY-1866-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: male
age (y): 32
pmi (hr): 19
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 0.6106257 22562 3.678E-38 19 22 657.7349 922.2512 8724 13838
cg00002426 0.07421676 13657 3.678E-38 19 19 1239.763 100.9429 12636 1021
cg00003994 0.01092032 13819 3.678E-38 11 10 1537.105 28.04056 13667 152
cg00005847 0.1312389 16770 3.678E-38 19 22 764.8721 196.3799 14556 2214
cg00006414 0.02560852 7788 3.678E-38 25 20 345.6 25.2 7586 202
cg00007981 0.01896733 15084 3.678E-38 22 27 1276.646 34.75172 14796 288
cg00008493 0.9806837 20815 3.678E-38 17 21 31.77217 1347.043 304 20511
cg00008713 0.01991692 25657 3.678E-38 16 19 1725 61.25 25144 513
cg00009407 0.04657827 26071 3.678E-38 18 28 1809.722 135.0574 24852 1219
cg00010193 0.6104662 41768 3.678E-38 24 15 1186.165 1362.12 16209 25559
cg00011459 0.9438545 17604 3.678E-38 22 25 107.6664 1161.304 894 16710
cg00012199 0.007631375 20604 3.678E-38 16 23 1276.75 19 20446 158
cg00012386 0.01188293 26072 3.678E-38 21 22 2064.56 37.96991 25761 311
cg00012792 0.0167918 37061 3.678E-38 16 22 2919.75 78.25 36437 624
cg00013618 0.8949013 21023 3.678E-38 20 19 166.5871 1190.035 2120 18903
cg00014085 0.01751254 20628 3.678E-38 20 19 1314.808 39.5784 20265 363
cg00014837 0.8913889 10700 3.678E-38 18 22 123.7437 840.5143 1073 9627
cg00015770 0.1108819 28011 3.678E-38 18 27 1966.935 227.6884 24894 3117
cg00016968 0.852594 35482 3.678E-38 13 12 505.3319 2039.078 5145 30337
cg00019495 0.04716368 16841 3.678E-38 28 16 1029.953 41.76508 16042 799

Total number of rows: 27578

Table truncated, full table size 1908 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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