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Sample GSM60606 Query DataSets for GSM60606
Status Public on Nov 14, 2005
Title Mouse-in vitro-4h-GC
Sample type RNA
 
Source name Mouse, thymus
Organism Mus musculus
Characteristics mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, cultivated in vitro under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 4h
Growth protocol cultivated in vitro under standard conditions (37°C, 5% CO2, saturated humidity)
Extracted molecule total RNA
Extraction protocol For total RNA isolation, TRIreagent (MRC Inc., Cincinnati, OH,USA) was used according to the manufacturer’s protocol. Briefly, up to 1x10E7 cells per ml were lysed with TRIreagent, 200ul of chloroform were added, the mixture centrifuged, and the RNA from the aqueous phase precipitated with isopropanol. The pelleted RNA was washed in 70% ethanol in DEPC-water and resuspended in nuclease-free water. RNA quantity and purity was determined by optical densitiy measurements (OD260/280) and RNA inte Glucocorticoid-receptority by using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA,USA), and only high quality RNA was further processed.
Label R-Phycoerythrin
Label protocol The chips were stained and washed in an Affymetrix fluidic station 450 following the EukGE-ws2v4 protocol.
 
Hybridization protocol On rotation (60 rpm) hybridization at 45C for 16 hours
Scan protocol Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GCOS software (version 1.2).
Description mus musculus, three CD-1 mice (males, aged 4-6 weeks), pooled thymic cell suspensions, cultivated in vitro under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 4h
Data processing Data processing and analysis was performed in R using Bioconductor version 1.5. GeneChip raw expression values were normalized and summarized using the robust multiarray analysis (RMA) method proposed by R. Irizarry.
 
Submission date Jun 09, 2005
Last update date Aug 28, 2018
Contact name Johannes Rainer
E-mail(s) johannes.rainer@eurac.edu
Organization name EURAC
Department Center for Biomedicing
Lab Biomedical Informatics
Street address Via Galvani 31
City Bolzano
ZIP/Postal code 39100
Country Italy
 
Platform ID GPL1261
Series (1)
GSE2843 thymic mouse cells
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMA normalized expression values

Data table
ID_REF VALUE
1415670_at 237.356212374567
1415671_at 733.823858068633
1415672_at 889.46868250499
1415673_at 327.635982749489
1415674_a_at 276.824917859936
1415675_at 230.424450490444
1415676_a_at 735.91228075768
1415677_at 132.93894503334
1415678_at 587.461298117399
1415679_at 1120.94517277162
1415680_at 545.90647546348
1415681_at 495.963451729131
1415682_at 242.309977322366
1415683_at 1038.79841318066
1415684_at 163.500359765314
1415685_at 253.624446275105
1415686_at 260.586764606683
1415687_a_at 2090.45315640716
1415688_at 622.966165678091
1415689_s_at 230.969733238853

Total number of rows: 45101

Table truncated, full table size 1246 Kbytes.




Supplementary file Size Download File type/resource
GSM60606.CEL.gz 5.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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