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Sample GSM1193119 Query DataSets for GSM1193119
Status Public on May 09, 2014
Title PBMC_Ctrl_subj3
Sample type RNA
 
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 total RNA
Extraction protocol Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.24.0).
 
Submission date Jul 19, 2013
Last update date May 10, 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 GPL11532
Series (2)
GSE49058 Aging-induced differential methylation in human PBMCs occurs with but often without change in expression of the associated gene (Expression)
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 RMA signal (as log2)

Data table
ID_REF VALUE
7892501 4.870076806
7892502 4.172911162
7892503 2.772064296
7892504 6.899953713
7892505 2.561548213
7892506 5.916779582
7892507 4.893131039
7892508 6.631876926
7892509 10.17547173
7892510 5.424553555
7892511 4.220404217
7892512 4.624490975
7892513 4.496377401
7892514 10.17144964
7892515 8.825557051
7892516 3.382550402
7892517 5.566995481
7892518 2.610347426
7892519 4.490212586
7892520 7.870660876

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1193119_G068_A09_03_03_CTRL.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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