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Sample GSM564620 Query DataSets for GSM564620
Status Public on Aug 04, 2011
Title AML with normal karyotype #12
Sample type RNA
 
Source name mononuclear cells from bone marrow
Organism Homo sapiens
Characteristics genotype/variation (cebpa single mutant, cebpa double mutant): negative,positive
Treatment protocol Samples are from untreated patients (de novo AML)
Extracted molecule total RNA
Extraction protocol The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols.
Label Biotin
Label protocol For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
 
Hybridization protocol Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
Scan protocol Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
Description CEBPAdm
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default settings and targeted intensity values at 100. Intensity values were log2 transformed and mean centered per probe set.
 
Submission date Jul 09, 2010
Last update date Aug 04, 2011
Contact name Erdogan Taskesen
Organization name Erasmus University Medical Center (EMC)
Street address dr. molewaterplein 50
City Rotterdam
ZIP/Postal code 3015GE
Country Netherlands
 
Platform ID GPL570
Series (1)
GSE22845 Gene expression profiling of CEBPA double-, single-mutant and CEBPA wild type AML

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity, log2 transformed and mean centered per probe set

Data table
ID_REF VALUE
1007_s_at -1.032
1053_at -0.54442
117_at 1.3112
121_at 0.05703
1255_g_at 0.95637
1294_at 0.62824
1316_at -0.22841
1320_at 0.59167
1405_i_at 1.8728
1431_at 0.37249
1438_at 0.21889
1487_at 0.37989
1494_f_at -0.26742
1552256_a_at -0.4964
1552257_a_at -0.10236
1552258_at 1.6975
1552261_at 0.62681
1552263_at -0.8331
1552264_a_at -0.38399
1552266_at 1.2767

Total number of rows: 54675

Table truncated, full table size 1002 Kbytes.




Supplementary file Size Download File type/resource
GSM564620.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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