NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1193126 Query DataSets for GSM1193126
Status Public on May 09, 2014
Title PBMC_Ctrl_subj12
Sample type RNA
 
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 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 4.512335779
7892502 3.861369403
7892503 3.087433278
7892504 6.75325794
7892505 2.930853274
7892506 6.018265882
7892507 4.871399975
7892508 6.838835495
7892509 10.21869447
7892510 5.533650761
7892511 4.013311298
7892512 4.873226201
7892513 3.867246871
7892514 10.13221033
7892515 8.385795912
7892516 2.915531897
7892517 5.819442023
7892518 2.976439215
7892519 3.8042115
7892520 7.662621998

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM1193126_G068_D09_12_12_CTRL.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap