Feb 09, 2023
Multimodal imaging pipeline for molecular and cellular characterization of Liver tissue - HuBMAP TTD-Columbia/PSU
- Presha Rajbhandari1,
- Hua Tian2,
- Aubrianna Decker1,
- Taruna Neelakantan1,
- Brent Stockwell1
- 1Columbia University;
- 2Pennsylvania State University
- Presha Rajbhandari: * co-first author;
- Hua Tian: * co-first author
- Human BioMolecular Atlas Program (HuBMAP) Method Development Community
- Hubmap TTD Columbia/PSU
Protocol Citation: Presha Rajbhandari, Hua Tian, Aubrianna Decker, Taruna Neelakantan, Brent Stockwell 2023. Multimodal imaging pipeline for molecular and cellular characterization of Liver tissue - HuBMAP TTD-Columbia/PSU. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygx913zg8j/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 09, 2023
Last Modified: February 09, 2023
Protocol Integer ID: 76756
Keywords: cellular characterization of liver tissue, spatial organization of liver tissue, multimodal imaging pipeline, human biomolecular atlas program, multimodal imaging on consecutive tissue section, multimodal imaging workflow, liver tissue, performing multimodal imaging, multimodal imaging, metabolic heterogeneity at tissue, rnascope, single cell level resolution, cellular characterization, hubmap ttd, imaging, hubmap, metabolic heterogeneity
Funders Acknowledgements:
NIH Hubmap
Grant ID: 4UH3CA256962
Abstract
We have developed a workflow to assess the spatial organization of liver tissue with regard to its cellular and metabolic heterogeneity at tissue and single cell level resolution - by performing multimodal imaging on consecutive tissue sections using H&E staining, DESI, (H2O)n-GCIB-SIMS, C60-SIMS, and RNAscope.
This document provides the collection of protocols within the multimodal imaging workflow implemented by Columbia University/Pennsylvania State University Transformative Technology Development Center as a part of Human Biomolecular Atlas Program (HuBMAP, NIH).
Troubleshooting
Acquire human tissue blocks.
Prepare tissue sections for multimodal imaging on appropriate substrates.
dx.doi.org/10.17504/protocols.io.e6nvwjmjzlmk/v1
H&E staining is performed using standard protocol.
DESI-IMS is performed as described here.
(H2O)n-GCIB-SIMS-IMS is performed as described here.
C60-SIMS for multiplexed antibody staining is performed as described here.
RNAScope imaging is performed as described here.