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Sample GSM60607 Query DataSets for GSM60607
Status Public on Nov 14, 2005
Title Mouse-in vitro-4h-EtOH
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 ethanol 0.1% 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 ethanol 0.1% 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 233.824128469478
1415671_at 725.272833120656
1415672_at 937.82179663236
1415673_at 236.277755146746
1415674_a_at 295.847521796679
1415675_at 218.404685965389
1415676_a_at 712.67968965693
1415677_at 144.037434668759
1415678_at 578.972092837145
1415679_at 1121.64467292185
1415680_at 471.783122985572
1415681_at 465.423420506845
1415682_at 222.103759032254
1415683_at 957.626987405211
1415684_at 118.882289892260
1415685_at 290.722717507566
1415686_at 269.118917981896
1415687_a_at 2301.08729509820
1415688_at 608.022119994797
1415689_s_at 210.526786952273

Total number of rows: 45101

Table truncated, full table size 1247 Kbytes.




Supplementary file Size Download File type/resource
GSM60607.CEL.gz 5.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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