Getting the right cells to the array: Gene expression microarray analysis of cell mixtures and sorted cells

Abstract

Background: Most biological samples are cell mixtures. Some basic questions are still unanswered about analyzing these heterogeneous samples using gene expression microarray technology (MAT). How meaningful is a cell mixture's overall gene expression profile (GEP)? Is it necessary to purify the cells of interest before microarray analysis, and how much purity is needed? How much does the purification itself distort the GEP, and how well can the GEP of a small cell subset be recovered? Methods: Model cell mixtures with different cell ratios were analyzed by both spotted and Affymetrix MAT. GEP distortion during cell purification and GEPs of purified cells were studied. CD34ϩ cord blood cells were purified and analyzed by MAT. Results: GEPs for mixed cell populations were found to mirror the cell ratios in the mixture. Over 75% pure

Distinct molecular phenotype of malignant CD34+ hematopoietic stem and progenitor cells in chronic myelogenous leukemia

“…However, mononuclear cells are a heterogenous cell population consisting of a broad spectrum of partially and completely differentiated cell types. Therefore, the expression pattern might only reflect the different proportions of the leukocyte subtypes in normal and CML mononuclear cells (Szaniszlo et al, 2004). In order to compare similar cell subsets, to analyse a more homogenous cell population and to examine cells which are closer to the cell of origin in CML, we examined highly enriched CD34 þ hematopoietic stem and progenitor cells.…”

Acquisition of Host-Derived CD40L by HIV-1In Vivoand Its Functional Consequences in the B-Cell Compartment

“…It is possible that the use of this transfection-and-expression system yields virus particles bearing amounts of host-derived CD40L higher than the levels found in virions circulating in patient plasma. However, the use of such an artificial system was necessary, as transcriptome analysis using microarrays requires a high degree of cellular and stimulus homogeneity to yield significant data (53). Although it is quite likely that circulating HIV-1 particles carry smaller amounts of incorporated CD40L molecules in the context of a natural infection, it also is true that the B-cell compartment will be exposed to CD40L-bearing viruses in a chronic manner during extended periods of time.…”

Polymer-Based Microfluidic Devices for Pharmacy, Biology and Tissue Engineering

“…Flow sorting has shown the benefit of isolating large numbers of specific chromosomes from humans during the human genome sequencing project, as well as for other primates [240], plant species [241], and more recently in the production of chromosome paints [242]. Flow sorters have also shown their advantages to sort specific subsets of cells for microarray analysis [243], to sort single particles into individual wells of a plate for cloning [244] and to perform polymerase chain reaction (PCR) analysis [245]. To enable cell transport or sorting on microfabricated chips [246], hydrodynamic [247,248] electro-kinetic [42], electro-osmotic [173,249] and DEP forces [177,194] have been used.…”