Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis

Akanksha Bafna; Petrina Lau; Gareth Banks; Patrick M Nolan

doi:10.1016/j.xpro.2023.102618

Harvesting mouse suprachiasmatic nucleus by vibrating microtome for diurnal transcriptome analysis

STAR Protoc. 2023 Dec 15;4(4):102618. doi: 10.1016/j.xpro.2023.102618. Epub 2023 Sep 26.

Authors

Akanksha Bafna¹, Petrina Lau², Gareth Banks³, Patrick M Nolan⁴

Affiliations

¹ Medical Research Council, Harwell Science Campus, Oxfordshire, UK. Electronic address: a.bafna@har.mrc.ac.uk.
² Medical Research Council, Harwell Science Campus, Oxfordshire, UK; Wolfson Institute for Biomedical Research, University College London, London, UK.
³ Medical Research Council, Harwell Science Campus, Oxfordshire, UK.
⁴ Medical Research Council, Harwell Science Campus, Oxfordshire, UK. Electronic address: pmnolan10@gmail.com.

Abstract

The mammalian suprachiasmatic nucleus (SCN) is the principal circadian clock that synchronizes daily behavioral and physiological responses in response to environmental cues. Here, we present a protocol for harvesting mouse SCN by vibrating microtome for diurnal transcriptome analysis. We describe steps for mouse entrainment, isolation of the SCN, tissue preparation, slicing with a vibratome, and handling of the harvested SCN for RNA extraction. This protocol can also be used for harvesting other mammalian brain regions for genomic studies.

Keywords: Genetics; Model Organisms; Molecular Biology; Neuroscience.

MeSH terms

Animals
Circadian Clocks*
Circadian Rhythm* / genetics
Gene Expression Profiling
Histological Techniques
Mammals
Mice
Suprachiasmatic Nucleus / physiology

Grants and funding

MC_U142684173/MRC_/Medical Research Council/United Kingdom