Transcriptomics

Dataset Information

2

Transcription profiling by array of blood and bone marrow samples obtained from patients suffering from acute myeloid leukemia (AML, subtype M1 and M2)


ABSTRACT: Acute myeloid leukemia (AML) is the most common and severe acute leukemia in adults. It is a heterogeneous disease where the subset of molecularly different types, presenting various morphological features and differentiation stage, can be distinguished. Genomic research of leukemias is conducted since 1999 and large cohort studies shown that particular genetic alterations correspond with specific gene expression signatures. However, not always they provide clinically relevant information. The most unknown group is cytogenetically normal acute myeloid leukemia (CN-AML, 40-49% of all AML cases). The aim of our experiment was to determine selected gene expression profiles in CN-AML, using small, boutique microarray. The array contained 933 oligonucleotide probes, mainly complementary to acute myeloid leukemia markers, genes involved in leukemic transformation and myeloid cell proliferation, differentiation and maturation. Our test dataset included 40 hybridizations: 24 corresponding with blood and bone marrow samples collected from 12 patients with AML M1 or M2 FAB subtype and 16 corresponding with healthy control samples. Total RNA was extracted from the mononuclear cell fractions, reversibly transcribed to cDNA and labeled with Alexa 647 dye. The common reference was RNA isolated from HL-60 cell culture, labeled with Alexa 555 dye.

ORGANISM(S): Homo sapiens  

DISEASE(S): Acute Myeloid Leukemia,Acute Promyelocytic Leukemia,Normal

SUBMITTER: Luiza Handschuh  

PROVIDER: E-MEXP-3647 | ArrayExpress | 2013-07-01

REPOSITORIES: ArrayExpress

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Publications

Analysis of boutique arrays: a universal method for the selection of the optimal data normalization procedure.

Uszczyńska Barbara B   Zyprych-Walczak Joanna J   Handschuh Luiza L   Szabelska Alicja A   Kaźmierczak Maciej M   Woronowicz Wiesława W   Kozłowski Piotr P   Sikorski Michał M MM   Komarnicki Mieczysław M   Siatkowski Idzi I   Figlerowicz Marek M  

International journal of molecular medicine 20130715 3


DNA microarrays, which are among the most popular genomic tools, are widely applied in biology and medicine. Boutique arrays, which are small, spotted, dedicated microarrays, constitute an inexpensive alternative to whole-genome screening methods. The data extracted from each microarray-based experiment must be transformed and processed prior to further analysis to eliminate any technical bias. The normalization of the data is the most crucial step of microarray data pre-processing and this proc  ...[more]

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