Comparison of RNA-Seq and microarray methods of transcriptome analysis in Human macrophages

Macrophages are dynamic cells integrating signals from their microenvironment to develop specific functional responses. Although, microarray-based transcriptional profiling has established transcriptional reprogramming as an important mechanism for signal integration and cell function of macrophages, current knowledge on transcriptional regulation of human macrophages is far from complete.

Researchers at University of Bonn, Germany performed RNA sequencing (RNA-Seq) of human macrophages to discover novel marker genes, an area of great need particularly in human macrophage biology, and also to generate a much more thorough transcriptome of human M1- and M1-like macrophages, we. Using RNA-Seq, they identified important gene clusters so far not appreciated by standard microarray techniques. In addition, they were able to detect differential promoter usage, alternative transcription start sites, and different coding sequences for 57 gene loci in human macrophages. Moreover, this approach led to the identification of novel M1-associated (CD120b, TLR2, SLAMF7) as well as M2-associated (CD1a, CD1b, CD93, CD226) cell surface markers.

Taken together, these data support that high-resolution transcriptome profiling of human macrophages by RNA-Seq leads to a better understanding of macrophage function and will form the basis for a better characterization of macrophages in human health and disease.

  • Beyer M, Mallmann MR, Xue J, Staratschek-Jox A, Vorholt D, Krebs W, Sommer D, Sander J, Mertens C, Nino-Castro A, Schmidt SV, Schultze JL. (2012) High-Resolution Transcriptome of Human Macrophages. PLoS One 7(9), e45466. [article]
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