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Sample GSM60605 Query DataSets for GSM60605
Status Public on Nov 14, 2005
Title Mouse-in vivo-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, 4h after intraperitoneal injection of 0.2mg dexamethasone per mouse.
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, 4h after intraperitoneal injection of 0.2mg dexamethasone per mouse.
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 256.924382432005
1415671_at 538.924737495416
1415672_at 826.539524765592
1415673_at 152.447639331118
1415674_a_at 223.046391840778
1415675_at 193.112802319336
1415676_a_at 841.523645863585
1415677_at 153.461186056725
1415678_at 515.922301418671
1415679_at 1118.22903884355
1415680_at 431.737321012754
1415681_at 414.397072228750
1415682_at 179.223995985115
1415683_at 957.626987405211
1415684_at 153.824340822328
1415685_at 100.388486036943
1415686_at 329.396176795651
1415687_a_at 2483.57052555626
1415688_at 599.202569438355
1415689_s_at 151.744456189302

Total number of rows: 45101

Table truncated, full table size 1246 Kbytes.




Supplementary file Size Download File type/resource
GSM60605.CEL.gz 5.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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