GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM838427 Query DataSets for GSM838427
Status Public on Nov 24, 2011
Title TEX, triplicate 3
Sample type RNA
Source name TEX cells
Organism Homo sapiens
Characteristics cell line: TEX
treatment: DMSO
leukemia type: AML
Treatment protocol Cells were treated with DMSO
Growth protocol TEX cells were maintained in IMDM, 15% FBS, 2 mM L-glutamine, 1% Pen/Strep, 20 ng/mL SCF, 2 ng/mL IL3. M9-ENL1 cells were maintained in MEM, 20% FBS, 5% human adult plasma, 2mM L-glutamine, 1% Pen/Strep, 100 ng/mL SCF, 10 ng/mL IL3, 5 ng/mL IL7, 5 ng/mL FLT3-ligand.
Extracted molecule total RNA
Extraction protocol TriZol extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
Hybridization protocol The cDNA was fragmented, labeled and hybridized to Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA)
Scan protocol standard Affymetrix protocol
Data processing The data was processed using Bioconductor (affy package 1.30.0) by reading CEL files with default 'ReadAffy()' function. Data was background corrected with RMA, normalized by quantiles method, PM only correction, and then median polished. To account for batch variation, the log2 values were adjusted using ComBat (version 2) in GenePattern with a parametric Empirical Bayes priors distribution estimation method and without covariate analysis.
Submission date Nov 22, 2011
Last update date Nov 28, 2011
Contact name Kolja Eppert
Organization name University Health Network
Street address 101 College St., rm 8-301
City Toronto
State/province Ontario
ZIP/Postal code M5G 1L7
Country Canada
Platform ID GPL571
Series (1)
GSE33892 Comparison of TEX and M9-ENL1 cell lines to HL60 and THP1 cell lines

Data table header descriptions
VALUE log2 transformed intensity value

Data table
1007_s_at 6.214802202
1053_at 8.516522749
117_at 6.131559051
121_at 8.302782803
1255_g_at 4.409959058
1294_at 7.684620831
1316_at 5.641817037
1320_at 4.9851684
1405_i_at 6.998618835
1431_at 4.723246585
1438_at 6.123173244
1487_at 7.824781088
1494_f_at 6.577277238
1598_g_at 7.831295998
160020_at 6.835036338
1729_at 7.164542548
177_at 5.324121526
1773_at 7.046480146
179_at 8.643425945
1861_at 6.358883437

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM838427_C.CEL.gz 1.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap