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Sample GSM387078 Query DataSets for GSM387078
Status Public on Jan 01, 2010
Title AML with normal karyotype #19
Sample type RNA
Source name mononuclear cells from bone marrow
Organism Homo sapiens
Characteristics npm1: positive
flt3-itd: negative
cebpa: n./a.
age: 52
diagnosis: AML with normal karyotype
gender: female
specimen type: Bone Marrow
blast cell percentage: 68
disease state: de novo AML
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 DRE
Data processing The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.20.2) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
Submission date Mar 27, 2009
Last update date Nov 14, 2018
Contact name Hans-Ulrich Klein
Organization name Columbia University Medical Center
Department Neurology
Lab Center for Translational and Computational Neuroimmunology
Street address 622 W 168th St
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platform ID GPL570
Series (1)
GSE15434 Gene expression profiling in AML with normal karyotype: A multicenter study investigating molecular markers in 251 cases
Reanalyzed by GSE119087
Reanalyzed by GSE122511

Data table header descriptions
VALUE The Robust Multichip Average (RMA) expression measure

Data table
1007_s_at 3.906161594
1053_at 5.591188047
117_at 3.354312947
121_at 6.553781451
1255_g_at 2.203350551
1294_at 7.393756678
1316_at 5.141316861
1320_at 2.622576965
1405_i_at 8.645358768
1431_at 2.431755097
1438_at 2.833693276
1487_at 5.477569468
1494_f_at 4.347772057
1552256_a_at 6.467099022
1552257_a_at 7.340264566
1552258_at 4.09304537
1552261_at 2.78416495
1552263_at 6.273372582
1552264_a_at 6.490228291
1552266_at 2.33388628

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM387078.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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