Shujun Ge, Wenqi Gan, Keaton Karlinsey, Beiyan Zhou, Joel S Pachter
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引用次数: 0
Abstract
Background: Laser capture microdissection (LCM), when combined with immunostaining (immuno-LCM) and coupled to RNA profiling, provides a means for in situ transcriptomic interrogation of complex tissues. However, preserving RNA integrity through the multiple harsh steps of immuno-LCM has proved challenging, greatly limiting the potential for high-resolution spatial analysis of global gene expression.
New method: Here, we describe a protocol whereby perfusion fixation and subsequent ex vivo post-fixation of mouse brain with paraformaldehyde, followed by protease digestion of immuno-LCM-acquired material from brain sections, allows for isolation of RNA of relatively high integrity that is amenable to RNA-seq with minimal technical variability.
Results: The individual steps of the fixation/immuno-LCM protocol were evaluated for their respective effects on RNA integrity and found not to produce significant compromise, as judged by RIN values determined using a Bioanalyzer or Tape Station. Utilizing the fixation/immuno-LCM protocol to assess gene expression from targeted brain microvascular tissue further showed high reproducibility in both qRT-PCR and RNA-seq analysis, as determined by interpolation and Pearson Correlation, respectively, with the latter detecting ∼ 22,000 genes, including those in the established blood-brain barrier transcriptome.
Comparison with existing methods: To date, there has been no detailed analysis of how fixation combined with immuno-LCM impacts RNA integrity and transcriptomic analysis.
Conclusions: The rigorous analyses performed demonstrate that paraformaldehyde fixation - which covalently cross-links RNA and protein - can be reversed without significant damage to RNA integrity, and can be combined with immuno-LCM to enable high-resolution spatial analysis of global gene expression.
期刊介绍:
The Journal of Neuroscience Methods publishes papers that describe new methods that are specifically for neuroscience research conducted in invertebrates, vertebrates or in man. Major methodological improvements or important refinements of established neuroscience methods are also considered for publication. The Journal''s Scope includes all aspects of contemporary neuroscience research, including anatomical, behavioural, biochemical, cellular, computational, molecular, invasive and non-invasive imaging, optogenetic, and physiological research investigations.