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Sample GSM822479 Query DataSets for GSM822479
Status Public on Jun 15, 2012
Title MLD, biallelic AML MLL_00261
Sample type RNA
 
Source name MLL_00261
Organism Homo sapiens
Characteristics ID: MLL_00261
cell type: PBMC
disease state: Multilineage dysplasia, acute myeloid leukemia, biallelic
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 MLD, biallelic
Data processing The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) 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 Oct 25, 2011
Last update date Jun 15, 2012
Contact name Andreas Roller
Organization name Munich Leukemia Laboratory
Street address Max-Lebsche-Platz 31
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL570
Series (1)
GSE33223 Multilineage dysplasia does not influence prognosis in patients with CEBPA mutated AML supporting the WHO proposal to classify these patients as a unique entity

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

Data table
ID_REF VALUE
1007_s_at 5.15247558
1053_at 8.053565768
117_at 4.911019503
121_at 7.064413033
1255_g_at 2.57297792
1294_at 9.613569252
1316_at 5.484780778
1320_at 3.617282738
1405_i_at 8.829613401
1431_at 4.53802503
1438_at 4.857031572
1487_at 7.80621848
1494_f_at 5.396656548
1552256_a_at 8.017447859
1552257_a_at 8.502484583
1552258_at 5.736684612
1552261_at 3.855064131
1552263_at 8.364029552
1552264_a_at 8.619495973
1552266_at 2.706253605

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM822479_MLL_00261_HG-U133_Plus_2_.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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