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Sample GSM822489 Query DataSets for GSM822489
Status Public on Jun 15, 2012
Title no MLD, biallelic AML MLL_00264
Sample type RNA
 
Source name MLL_00264
Organism Homo sapiens
Characteristics ID: MLL_00264
cell type: PBMC
disease state: no 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 no 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 5.010499901
1053_at 7.966744796
117_at 5.674198003
121_at 7.120681951
1255_g_at 2.716638646
1294_at 9.493244868
1316_at 5.215308437
1320_at 3.953449406
1405_i_at 11.09363628
1431_at 5.103952134
1438_at 4.621615318
1487_at 7.373872537
1494_f_at 5.440574571
1552256_a_at 7.373612974
1552257_a_at 8.655140535
1552258_at 5.711575444
1552261_at 3.707053506
1552263_at 8.042114964
1552264_a_at 8.325279589
1552266_at 2.515222112

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM822489_MLL_00264_HG-U133_Plus_2_.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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