Fragmentation of tissue-resident macrophages during isolation confounds analysis of single-cell preparations from mouse hematopoietic tissues
Susan Millard, Ostyn Heng, Khatora S. Opperman, Anuj Sehgal, Katharine M. Irvine, Simranpreet Kaur, Cheyenne J. Sandrock, Andy Wu, Graham Magor, Lena Batoon, Andrew C. Perkins, Jacqueline E. Noll, Andrew C.W. Zannettino, David P. Sester, Jean-Pierre Lévesque, David Hume, Liza J. Raggatt, Kim Summers, Allison R. Pettit
Abstract
remnant attachment. Remnant-restricted macrophage-specific membrane markers, cytoplasmic fluorescent reporters, and mRNA are all detected in non-macrophage cells including isolated stem and progenitor cells. Analysis of RNA sequencing (RNA-seq) data, including publicly available datasets, indicates that macrophage fragmentation is a general phenomenon that confounds bulk and single-cell analysis of disaggregated hematopoietic tissues. Hematopoietic tissue macrophage fragmentation undermines the accuracy of macrophage ex vivo molecular profiling and creates opportunity for misattribution of macrophage-expressed genes to non-macrophage cells.