RNA Detection

Chapter 6

LCM-Seq: A Method for Spatial Transcriptomic

Profiling Using Laser Capture Microdissection Coupled

with PolyA-Based RNA Sequencing

Susanne Nichterwitz, Julio Aguila Benitez, Rein Hoogstraaten,

Qiaolin Deng, and Eva Hedlund

Abstract

LCM-seq couples laser capture microdissection of cells from frozen tissues with polyA-based RNA
sequencing and is applicable to single neurons. The method utilizes off-the-shelf reagents and direct lysis
of the cells without RNA purification, making it a simple and relatively cheap method with high reproduc-
ibility and sensitivity compared to previous methods. The advantage with LCM-seq is also that tissue
sections are kept intact and thus the positional information of each cell is preserved.

Key wordsMotor neuron, Dopamine neuron, RNA sequencing, Laser capture microscopy, Smart-

seq2, HistoGene, Cresyl violet, Rapid antibody staining

1 Introduction

An ability to decipher gene expression within individual cells and/

or small, distinct neuronal populations will be fundamental to

improve our understanding of normal biological processes and

mechanisms of neuronal vulnerability to disease. Tissue samples

are often in scarcity, in particular patient samples, and cellular

heterogeneity can mask biological functions and/or disease path-

ways when tissues are analyzed as a whole or in bulks of hundreds to

thousands of cells. It is therefore vital that gene expression can be

studied in small tissue samples, minute cellular populations and

even in individual cells. Toward this goal, we have developed a

new method, LCM-seq, that combines laser capture microdissec-

tion/microscopy (LCM) with polyA-based Smart-seq2 RNA

sequencing [1]. This method allows for efficient and robust

Imre Gaspar (ed.),RNA Detection: Methods and Protocols, Methods in Molecular Biology,
vol. 1649, DOI 10.1007/978-1-4939-7213-5_6,©Springer Science+Business Media LLC 2018

Susanne Nichterwitz and Julio Aguila Benitez contributed equally to this work.

95