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Sample GSM1193240 Query DataSets for GSM1193240
Status Public on May 09, 2014
Title PBMC_Ctrl_subj3
Sample type genomic
 
Source name Peripheral blood mononuclear cells, 13hr incubation with 0.05% DMSO (control), subject 3
Organism Homo sapiens
Characteristics gender: male
subject: 3
age: 34 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
E-mail(s) guido.hooiveld@wur.nl
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
ID_REF
VALUE SWAN normalized beta values

Data table
ID_REF VALUE
cg00050873 0.812507989
cg00212031 0.108384057
cg00213748 0.810180276
cg00214611 0.049643881
cg00455876 0.741984578
cg01707559 0.122584423
cg02004872 0.031598513
cg02011394 0.966130449
cg02050847 0.977845439
cg02233190 0.086527294
cg02494853 0.039070515
cg02839557 0.048364876
cg02842889 0.047530144
cg03052502 0.976850947
cg03155755 0.932594214
cg03244189 0.118916207
cg03443143 0.880157038
cg03683899 0.031340487
cg03695421 0.718490305
cg03706273 0.033857166

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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