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Sample GSM531613 Query DataSets for GSM531613
Status Public on Jan 01, 2011
Title AML sample #14
Sample type RNA
 
Source name mononuclear cells after Ficoll purification
Organism Homo sapiens
Characteristics sample id: MLL_00082
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 Nov 14, 2018
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
Relations
Reanalyzed by GSE122511

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

Data table
ID_REF VALUE
1007_s_at 4.381643876
1053_at 6.014543816
117_at 3.64497341
121_at 6.426964104
1255_g_at 2.440875496
1294_at 8.089102584
1316_at 4.863345631
1320_at 3.292229694
1405_i_at 7.541873099
1431_at 3.350653085
1438_at 3.775418618
1487_at 5.99129215
1494_f_at 4.185052653
1552256_a_at 6.359243287
1552257_a_at 5.664698788
1552258_at 3.465383394
1552261_at 3.616748736
1552263_at 4.984093278
1552264_a_at 6.39227972
1552266_at 2.678354433

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM531613.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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