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Sample GSM60549 Query DataSets for GSM60549
Status Public on Nov 14, 2005
Title C-Line-CEMC1-ratGR-6h-GC
Sample type RNA
 
Source name rat- Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1
Organism Homo sapiens
Characteristics homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
Growth protocol cultured 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 biological source: homo sapiens, rat-Glucocorticoid-receptor transfected CCRF-CEM (ATCC no.: CLL-119) subclone C1, parental cell line C1 = GC resistant, C1-rat-GR = GC-sensitivity restored, cultured under standard conditions (37°C, 5% CO2, saturated humidity), in the presence of dexamethansone 10e-7M for 6h
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) [email protected]
Organization name Eurac Researc
Department Institute for Biomedicine
Lab Biomedical Informatics
Street address Via A. Volta 21
City Bolzano
ZIP/Postal code 39100
Country Italy
 
Platform ID GPL570
Series (1)
GSE2842 Additional systems to Prednisolone treated childhood ALL samples
Relations
Reanalyzed by GSE64985
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE RMA normalized expression values

Data table
ID_REF VALUE
1007_s_at 21.2933347072082
1053_at 283.642518298708
117_at 16.0430884923317
121_at 102.780302989089
1255_g_at 4.71415763124673
1294_at 100.221623277429
1316_at 18.2226389993808
1320_at 9.6467300819686
1405_i_at 6.56525023229372
1431_at 21.9812267687368
1438_at 15.9542623321057
1487_at 81.901047574504
1494_f_at 19.192756182145
1552256_a_at 191.534437650857
1552257_a_at 230.894500365057
1552258_at 10.0657306980360
1552261_at 12.4664604515318
1552263_at 156.903094965633
1552264_a_at 620.342002121742
1552266_at 5.19034342749593

Total number of rows: 54675

Table truncated, full table size 1480 Kbytes.




Supplementary file Size Download File type/resource
GSM60549.CEL.gz 7.7 Mb (ftp)(http) CEL

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