A fast and versatile method for simultaneous HCR, immunohistochemistry and EdU labeling (SHInE).
Aida ĆorićAlexander W StockingerPetra SchafferDunja RokvićKristin Tessmar-RaibleFlorian RaiblePublished in: Integrative and comparative biology (2023)
Access to newer, fast and cheap sequencing techniques, particularly on the single-cell level, have made transcriptomic data of tissues or single cells accessible to many researchers. As a consequence, there is increased need for in situ visualization of gene expression or encoded proteins to validate, localize or help interpret such sequencing data, as well as put them in context with cellular proliferation. A particular challenge for labeling and imaging transcripts are complex tissues that are often opaque and/or pigmented, preventing easy visual inspection. Here we introduce a versatile protocol that combines in situ hybridization chain reaction (HCR), immunohistochemistry (IHC) and proliferative cell labeling using 5-ethynyl-2'-deoxyuridine (EdU), and demonstrate its compatibility with tissue clearing. As a proof-of-concept, we show that our protocol allows for the parallel analysis of cell proliferation, gene expression and protein localization in bristleworm heads and trunks.
Keyphrases
- single cell
- gene expression
- rna seq
- cell proliferation
- dna methylation
- high throughput
- electronic health record
- randomized controlled trial
- induced apoptosis
- big data
- signaling pathway
- cell cycle arrest
- oxidative stress
- cell cycle
- stem cells
- pi k akt
- protein protein
- binding protein
- mass spectrometry
- small molecule
- mesenchymal stem cells
- data analysis
- artificial intelligence