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Sample GSM531687 Query DataSets for GSM531687
Status Public on Jan 01, 2011
Title AML sample #88
Sample type RNA
 
Source name mononuclear cells after Ficoll purification
Organism Homo sapiens
Characteristics sample id: MUC_00620
analysis i: AML-NOS
analysis ii: AML-NOS plus AML-MLD-sole
Treatment protocol Samples are from untreated AML patients.
Extracted molecule total RNA
Extraction protocol The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
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 AML samples investigated according to WHO 2008 classification
Data processing The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.22.0) 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 Apr 08, 2010
Last update date Jan 01, 2011
Contact name Hans-Ulrich Klein
E-mail(s) h.klein@uni-muenster.de
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)
GSE21261 Multilineage Dysplasia (MLD) in AML correlates with MDS-related cytogenetic abnormalities and a prior history of MDS or MDS/MPN but has no independent prognostic relevance

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

Data table
ID_REF VALUE
1007_s_at 4.512248418
1053_at 6.569804962
117_at 4.557362416
121_at 7.462160595
1255_g_at 2.417975539
1294_at 8.142311648
1316_at 5.022023829
1320_at 3.456640796
1405_i_at 10.11294993
1431_at 3.082175245
1438_at 4.100415215
1487_at 6.021917255
1494_f_at 4.748490295
1552256_a_at 6.877576503
1552257_a_at 7.777087234
1552258_at 4.235065587
1552261_at 3.872180241
1552263_at 6.209323777
1552264_a_at 7.331980202
1552266_at 2.986285617

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM531687.CEL.gz 7.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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