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Sample GSM838426 Query DataSets for GSM838426
Status Public on Nov 24, 2011
Title TEX, triplicate 2
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
ID_REF
VALUE log2 transformed intensity value

Data table
ID_REF VALUE
1007_s_at 6.162245954
1053_at 8.297212486
117_at 6.252602289
121_at 8.283629866
1255_g_at 4.282776226
1294_at 7.562040081
1316_at 5.417275197
1320_at 5.170360409
1405_i_at 6.608882991
1431_at 4.82430021
1438_at 5.977089876
1487_at 7.754445854
1494_f_at 6.129701054
1598_g_at 7.980255414
160020_at 7.00747927
1729_at 7.000199126
177_at 5.247178175
1773_at 6.918351284
179_at 8.585929136
1861_at 6.203955558

Total number of rows: 22277

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM838426_B.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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