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Sample GSM402051 Query DataSets for GSM402051
Status Public on Apr 20, 2010
Title UMARY-1230-TCTX-CpG
Sample type genomic
 
Source name Human Brain Tissue: TCTX
Organism Homo sapiens
Characteristics gender: female
age: 16
pmi: 16
tissuebank: UMARY
prep_hyb_batch: PLATE_V
tissue: temporal cortex
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: TCTX
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 15, 2009
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 (1)
GSE15745 Abundant Quantitative Trait Loci for CpG Methylation and Expression Across Human Brain Tissues

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 0.7420968 28085 3.678E-38 17 21 526.0598 925.5159 7169 20916
cg00002426 0.1620306 20859 3.678E-38 25 28 879.6 222.6 17463 3396
cg00003994 0.02853812 19628 3.678E-38 13 17 2402.129 114.2682 19065 563
cg00005847 0.1251486 25134 3.678E-38 20 18 880.34 233.4455 21976 3158
cg00006414 0.02436666 15413 3.678E-38 6 11 1317.417 77.56718 15035 378
cg00007981 0.01502753 20063 3.678E-38 16 24 909.25 64 19760 303
cg00008493 0.9860863 31236 3.678E-38 19 10 40.14775 869.9445 336 30900
cg00008713 0.01805833 37888 3.678E-38 19 16 863.5208 65.38348 37202 686
cg00009407 0.04897847 39938 3.678E-38 8 16 1022.83 290.6209 37977 1961
cg00010193 0.583338 72028 3.678E-38 22 18 1614.356 1415.866 29953 42075
cg00011459 0.9239421 21949 3.678E-38 18 17 151.0851 905.0967 1577 20372
cg00012199 0.005701719 24454 3.678E-38 12 10 1094.079 18.18653 24314 140
cg00012386 0.007571837 36615 3.678E-38 19 14 1951.869 31.42996 36337 278
cg00012792 0.01380046 64608 3.678E-38 19 16 2430.889 132.1435 63715 893
cg00013618 0.9072762 30809 3.678E-38 17 20 155.9504 1851.032 2766 28043
cg00014085 0.02385721 28361 3.678E-38 20 24 933.5584 43.60332 27682 679
cg00014837 0.9266503 13397 3.678E-38 20 17 132.3752 814.5995 890 12507
cg00015770 0.09755989 44980 3.678E-38 21 24 1507.449 171.0828 40582 4398
cg00016968 0.7084666 55211 3.678E-38 15 15 448.2333 1029.697 16025 39186
cg00019495 0.2502266 35212 3.678E-38 17 18 1416.651 595.425 26376 8836

Total number of rows: 27578

Table truncated, full table size 1917 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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