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Sample GSM401859 Query DataSets for GSM401859
Status Public on Apr 20, 2010
Title BLSA-1640-PONS-CpG
Sample type genomic
 
Source name Human Brain Tissue: PONS
Organism Homo sapiens
Characteristics gender: female
age: 96
pmi: 15
tissuebank: BLSA
prep_hyb_batch: PLATE_Z
tissue: pons
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: PONS
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 0.6251773 18234 3.678E-38 13 18 373.0359 654.5462 6772 11462
cg00002426 0.2020706 10718 3.678E-38 21 25 500.5918 176.9747 8532 2186
cg00003994 0.03159591 14174 3.678E-38 16 19 692.75 62.25 13723 451
cg00005847 0.5361422 14924 3.678E-38 16 21 343.75 248 6869 8055
cg00006414 0.03585605 7458 3.678E-38 15 20 451.0735 36.92244 7187 271
cg00007981 0.01581529 18047 3.678E-38 21 17 1013.404 25.09506 17760 287
cg00008493 0.9801819 22001 3.678E-38 11 15 51.85995 1282.328 338 21663
cg00008713 0.02354477 39739 3.678E-38 13 19 1329.062 81.81828 38801 938
cg00009407 0.05394996 31837 3.678E-38 11 16 1114.084 180.3038 30114 1723
cg00010193 0.5861159 55993 3.678E-38 22 16 1187.102 592.0584 23116 32877
cg00011459 0.9502062 9359 3.678E-38 12 18 56.29165 561.1844 371 8988
cg00012199 0.007914395 24665 3.678E-38 18 18 740.3408 16.97056 24469 196
cg00012386 0.02763327 32578 3.678E-38 19 17 1197.091 84.42499 31675 903
cg00012792 0.02750968 45593 3.678E-38 19 22 1937.645 136.7318 44336 1257
cg00013618 0.9042591 22346 3.678E-38 13 19 148.6597 880.5865 2049 20297
cg00014085 0.02190597 25829 3.678E-38 24 10 537.8671 45.92793 25261 568
cg00014837 0.8830352 7056 3.678E-38 16 21 84 297.75 737 6319
cg00015770 0.1097886 40396 3.678E-38 19 18 949.7811 234.4629 35950 4446
cg00016968 0.7552848 42096 3.678E-38 21 19 488.3716 899.4941 10226 31870
cg00019495 0.1958845 13750 3.678E-38 19 28 637.0875 179.6325 11037 2713

Total number of rows: 27578

Table truncated, full table size 1907 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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