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Sample GSM1193247 Query DataSets for GSM1193247
Status Public on May 09, 2014
Title PBMC_Ctrl_subj12
Sample type genomic
Source name Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 12
Organism Homo sapiens
Characteristics gender: male
subject: 12
age: 31 yr
age group: young
tissue: cultured peripheral blood mononuclear cells
treatment: 0.05% DMSO
Treatment protocol Peripheral blood mononuclear cells were incubated in RPMI1640 medium with 2 mmol/L L-glutamine, 10% fetal bovine serum and antibiotics (penicillin and streptomycin) in the presence of 5% CO2 at 37°C at 1.0 × 10^6 cells per ml with either WY14,643 (50 μM) or vehicle (DMSO, 0.05%). After 13 hrs of exposure the cell suspensions were transferred to 15ml tubes and centrifuged for 5 minutes at 1,600rpm at 4°C. The two cell pellets per donor were re-suspended in ice-cold PBS, and each transferred to separate eppendorf tubes for RNA and DNA isolation and again centrifuged for 5 minutes at 5,000rpm at 4°C. After removing the supernatant, pellets for DNA isolation were snap frozen on dry-ice and stored at -80°C. The pellets for RNA isolation were resuspended in 700 μL of Buffer RPE with added B-mercaptoethanol according to manufacturer’s instructions (Qiagen) and passed five times through a 23G needle before freezing at -80°C.
Growth protocol Peripheral blood mononuclear cells from ten healthy Caucasian male blood donors, aged 30, 31, 34, 35, 43, 52, 62, 64, 65 and 66 years, were isolated directly after arrival of the buffy coat (max. 8 hours after donation) by Ficol-paque Plus density gradient centrifugation (Amersham Biosciences, Roosendaal, the Netherlands). All donors gave full written informed consent.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from the PBMC pellets by using DNeasy Blood and Tissue Kit (Qiagen), including RNAse treatment, according to the manufacturer’s instructions. All samples were quality tested on a Nanodrop spectrophotometer prior to proceeding with the microarrays.
Label Cy3 and Cy5
Label protocol DNAs were prepared in a total volume of 20 μl (1 μg of FF) using a commercial kit EZ DNA Methylation kit (catalog number D5001; Zymo Research Corp, Orange, CA).
Hybridization protocol Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD Methylation Assay protocol
Scan protocol Arrays were imaged using HiScan Reader using standard recommended Illumina scanner settings
Data processing SWAN normalization on IDAT files using library minfi (v1.6.0) in R/Bioconductor, with beta-threshold = 0.001
Submission date Jul 19, 2013
Last update date May 09, 2014
Contact name Guido Hooiveld
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
Platform ID GPL13534
Series (2)
GSE49064 Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene (DNA Methylation)
GSE49065 Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene

Data table header descriptions
VALUE SWAN normalized beta values

Data table
cg00050873 0.837578663
cg00212031 0.051023243
cg00213748 0.803538603
cg00214611 0.066275963
cg00455876 0.719637342
cg01707559 0.138073191
cg02004872 0.033837626
cg02011394 0.961218107
cg02050847 0.961463181
cg02233190 0.064170866
cg02494853 0.039967997
cg02839557 0.053269933
cg02842889 0.045829583
cg03052502 0.978542223
cg03155755 0.935926581
cg03244189 0.087993023
cg03443143 0.880217455
cg03683899 0.044041386
cg03695421 0.593084037
cg03706273 0.036838689

Total number of rows: 485512

Table truncated, full table size 10861 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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