Open Access Open Badges Research article

Validation and implementation of a method for microarray gene expression profiling of minor B-cell subpopulations in man

Kim Steve Bergkvist1, Mette Nyegaard12, Martin Bøgsted1113, Alexander Schmitz1, Julie Støve Bødker1, Simon Mylius Rasmussen1, Martin Perez-Andres1, Steffen Falgreen1, Anders Ellern Bilgrau13, Malene Krag Kjeldsen1, Michael Gaihede114, Martin Agge Nørgaard5, John Bæch6, Marie-Louise Grønholdt7, Frank Svendsen Jensen8, Preben Johansen9, Karen Dybkær111 and Hans Erik Johnsen11011*

  • * Corresponding author: Hans E Johnsen

Author Affiliations

1 Department of Haematology, Aalborg University Hospital Science and Innovation Center, Sdr Skovvej 15, DK-9000 Aalborg, Denmark

2 Department of Biomedicine, Aarhus University, Aarhus, Denmark

3 Department of Mathematical Sciences, Aalborg University, Aalborg, Denmark

4 Department of Otolaryngology, Head & Neck Surgery, Aalborg University Hospital, Aalborg, Denmark

5 Cardiothoracic Surgery, Aalborg University Hospital, Aalborg, Denmark

6 Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark

7 Vascular Surgery, Aalborg University Hospital, Aalborg, Denmark

8 Abdominal Surgery, Aalborg University Hospital, Aalborg, Denmark

9 Pathology, Aalborg University Hospital, Aalborg, Denmark

10 The Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark

11 The Department of Clinical Medicine, Aalborg University, Aalborg, Denmark

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BMC Immunology 2014, 15:3  doi:10.1186/1471-2172-15-3

Published: 31 January 2014



This report describes a method for the generation of global gene expression profiles from low frequent B-cell subsets by using fluorescence-activated cell sorting and RNA amplification. However, some of the differentiating compartments involve a low number of cells and therefore it is important to optimize and validate each step in the procedure.


Normal lymphoid tissues from blood, tonsils, thymus and bone marrow were immunophenotyped by the 8-colour Euroflow panel using multiparametric flow cytometry. Subsets of B-cells containing cell numbers ranging from 800 to 33,000 and with frequencies varying between 0.1 and 10 percent were sorted, subjected to mRNA purification, amplified by the NuGEN protocol and finally analysed by the Affymetrix platform.


Following a step by step strategy, each step in the workflow was validated and the sorting/storage conditions optimized as described in this report. First, an analysis of four cancer cell lines on Affymetrix arrays, using either 100 ng RNA labelled with the Ambion standard protocol or 1 ng RNA amplified and labelled by the NuGEN protocol, revealed a significant correlation of gene expressions (r ≥ 0.9 for all). Comparison of qPCR data in samples with or without amplification for 8 genes showed that a relative difference between six cell lines was preserved (r ≥ 0.9). Second, a comparison of cells sorted into PrepProtect, RNAlater or directly into lysis/binding buffer showed a higher yield of purified mRNA following storage in lysis/binding buffer (p < 0.001). Third, the identity of the B-cell subsets validated by the cluster of differentiation (CD) membrane profile was highly concordant with the transcriptional gene expression (p-values <0.001). Finally, in normal bone marrow and tonsil samples, eight evaluated genes were expressed in accordance with the biology of lymphopoiesis (p-values < 0.001), which enabled the generation of a gene-specific B-cell atlas.


A description of the implementation and validation of commercially available kits in the laboratory has been examined. This included steps for cell sorting, cell lysis/stabilization, RNA isolation, RNA concentration and amplification for microarray analysis. The workflow described in this report will enable the generation of microarray data from minor sorted B-cell subsets.

Microarray gene expression profiling; RNA purification; B-cell subpopulations; Fluorescence activated cell sorting