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Sample GSM1193248 Query DataSets for GSM1193248
Status Public on May 09, 2014
Title PBMC_WY_subj1
Sample type genomic
Source name Peripheral blood mononuclear cells, 13hr incubation with 50 uM WY14,643, subject 1
Organism Homo sapiens
Characteristics gender: male
subject: 1
age: 43 yr
age group: young
tissue: cultured peripheral blood mononuclear cells
treatment: 50 uM WY14,643
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 0.816398337
cg00212031 0.050138759
cg00213748 0.787191125
cg00214611 0.064605562
cg00455876 0.756235154
cg01707559 0.127615572
cg02004872 0.054994075
cg02011394 0.954347748
cg02050847 0.964914046
cg02233190 0.056569937
cg02494853 0.046128987
cg02839557 0.055577532
cg02842889 0.039060505
cg03052502 0.981114497
cg03155755 0.921338077
cg03244189 0.086631984
cg03443143 0.868391131
cg03683899 0.034735747
cg03695421 0.679862094
cg03706273 0.048072467

Total number of rows: 485512

Table truncated, full table size 10862 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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