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Sample GSM60608 Query DataSets for GSM60608
Status Public on Nov 14, 2005
Title Mouse-untreated
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, without treatment
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, without treatment
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
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
Reanalyzed by GSE119085

Data table header descriptions
VALUE RMA normalized expression values

Data table
1415670_at 295.624084409766
1415671_at 558.82393347082
1415672_at 930.614593000848
1415673_at 207.825662456834
1415674_a_at 301.921565836058
1415675_at 184.431337408061
1415676_a_at 1011.42946675507
1415677_at 143.023658266525
1415678_at 530.022575446585
1415679_at 1105.58942029443
1415680_at 373.423781933996
1415681_at 465.423420506845
1415682_at 198.528180767004
1415683_at 942.468114599681
1415684_at 194.204120359196
1415685_at 176.482338188825
1415686_at 361.436902041097
1415687_a_at 2320.46785994025
1415688_at 825.823692994342
1415689_s_at 203.024496475397

Total number of rows: 45101

Table truncated, full table size 1246 Kbytes.

Supplementary file Size Download File type/resource
GSM60608.CEL.gz 5.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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