NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM401559 Query DataSets for GSM401559
Status Public on Apr 20, 2010
Title UMARY-5081-CRBLM-CpG
Sample type genomic
 
Source name Human Brain Tissue: CRBLM
Organism Homo sapiens
Characteristics tissue: cerebellum
gender: male
age (y): 48
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) [email protected]
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 0.5923024 8578 3.678E-38 22 16 229.1908 250.9372 3438 5140
cg00002426 0.0570561 6157 3.678E-38 20 24 435.586 32.64659 5800 357
cg00003994 0.03118251 7308 3.678E-38 11 21 501.7149 55.17657 7077 231
cg00005847 0.09950304 8955 3.678E-38 24 22 498.0629 71.23933 8054 901
cg00006414 0.03573837 5832 3.678E-38 11 19 496.5892 33.76927 5620 212
cg00007981 0.03158907 7181 3.678E-38 21 20 290.0116 30.76872 6951 230
cg00008493 0.9796582 19564 3.678E-38 27 18 24.24871 566.1882 300 19264
cg00008713 0.0191091 23135 3.678E-38 12 17 985.5369 52.82755 22691 444
cg00009407 0.05114736 17985 3.678E-38 15 25 815.1339 110.7673 17060 925
cg00010193 0.5527941 46856 3.678E-38 16 9 1623.75 1280.75 20899 25957
cg00011459 0.925814 5858 3.678E-38 18 23 41.955 379.7163 342 5516
cg00012199 0.01324503 13339 3.678E-38 22 8 687.5723 11.29964 13161 178
cg00012386 0.01019941 15195 3.678E-38 29 13 1052.707 18.38384 15039 156
cg00012792 0.01473918 25071 3.678E-38 24 21 713.618 48.78567 24700 371
cg00013618 0.9327403 14738 3.678E-38 12 19 44.74464 925.2038 898 13840
cg00014085 0.01772493 13271 3.678E-38 17 16 507.6271 30.31695 13034 237
cg00014837 0.81719 3658 3.678E-38 18 20 66.23234 266.1078 587 3071
cg00015770 0.07794639 20196 3.678E-38 22 20 993.3021 70.78264 18614 1582
cg00016968 0.9166823 26581 3.678E-38 10 20 163.4898 2148.135 2123 24458
cg00019495 0.05102367 6152 3.678E-38 9 19 961 58.33333 5833 319

Total number of rows: 27578

Table truncated, full table size 1884 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap