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Spatial Omics
Methods for Reconstructing the Spatial Heterogeneity of Biological Tissue
- 1st Edition - June 1, 2029
- Editor: Kieran Mcgourty
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 9 6 8 6 - 0
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 9 6 8 7 - 7
Spatial Omics: Methods for Reconstructing the Spatial Heterogeneity of Biological Tissue is a complete and detailed reference on research methods that combine the in-depth… Read more
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Request a sales quoteSpatial Omics: Methods for Reconstructing the Spatial Heterogeneity of Biological Tissue is a complete and detailed reference on research methods that combine the in-depth analysis at single cell level with context provided by tissue positioning. The methods covered in the book include Methods that require the mechanical tissue retrieval, digestion and enrichment, Methods based on in situ hybridization and imaging, Methods reliant on next generation sequencing and hybrid techniques, and Computational based methods to determine spatial relatedness of cells. Technologies are focused on the balance between sensitivity, accuracy, and extent of features through which single cells can be evaluated, and more.
Cellular and molecular biologists will benefit from the detailed experimental setup information included in this comprehensive book. Computational biologists and computer scientists involved in biological visualization problems can also use this book as a guide to interpret and analyze experimental data.
- Covers the methods currently available to reconstruct the spatial heterogeneity of biological tissues
- Provides all methods, including detailed and expansive templates on materials, equipment and steps involved to execute the experiments
- Authored by researchers from key laboratories around the world who pioneered techniques covered
Cellular and Molecular biologists, and Biochemistry researchers at PhD level and above
Computational Biologists, Computer Scientists involved in biological visualization problems, Data scientists involved in omics research
Computational Biologists, Computer Scientists involved in biological visualization problems, Data scientists involved in omics research
Introduction
1. Comment on Spatial Transcriptomics Landscape
2. Comment on Human Cell Atlas and CZI Initiatives
Targeted dissection coupled with gene expression
3. Manual dissection, digestion and enrichment followed by NGS
4. General comment introduction to cell targeted NGS
5. Laser capture microdissection (LCM-SEQ)
6. Laser capture microdissection with (geo-seq)
7. Serial cryo-sectioning TOMO-SEQ
8. In-vivo transcriptome assessment (TIVA)
In-situ hybridization and imaging-based approaches
9. Single-Molecule RNA fluorescence in situ hybridisation (smFISH)
10. Multiplexed Error-Robust hybridisation technology (merFISH)
11. Sequential Fluorescence In-Situ Hybridisation (seqFISH/seqFish+)
12. Ouroboros smFISH (osmFISH)
13. RNAscope (RNAscope) RNAscope Hiplex
14. Fluorescent in situ RNA sequencing
15. In situ transcriptome accessibility sequencing (INSTAseq) and Barcode in situ Sequencing (BaristaSeq)
In situ mRNA capture and next generation sequencing
16. Slide-Seq
17. High-definition spatial transcriptomics
18. Nanostring digital spatial profiling
19. APEX-Seq
20. Microfluidic barcoding
21. Targeted cell isolation and profiling (Probe-Seq)
Emerging multimodal spatial imaging
22. DNA microscopy New class of imaging. Amazing.
23. Mass-cytometry coupled to multimodal analysis
In-silico tools for spatial transcriptomics
24. SpaceTx and Starfish (amalgamation of imaging-based approaches)
25. Oligonucleotide-based spatial barcoding followed with NGS. Hierarchical Barcoding
26. Incorporation of labelling approaches and multi-omics
27. Incorporation of histological data/tissue atlas generation
28. Downstream analyses incorporating lineage multi-modal data incorporation
- No. of pages: 350
- Language: English
- Edition: 1
- Published: June 1, 2029
- Imprint: Academic Press
- Paperback ISBN: 9780323996860
- eBook ISBN: 9780323996877
KM
Kieran Mcgourty
Dr. McGourty is a lecturer in the Chemical Sciences department at the University of Limerick (UL). Kieran undertook his undergraduate studies at UL, in Industrial Biochemistry, where he worked with Dr. Jakki Cooney and Dr. Todd Kagawa. In 2006, motivated by these experiences, he went on to attain a Wellcome Trust funded PhD working with Prof. David Holden FRS, Imperial College London, studying the molecular basis of infection. During this time, Kieran published several high impact papers on the intracellular interaction of Salmonella Typhimurium with the host before changing field from cellular microbiology to cell biology.
His research group primarily focusses on the architectures of both diseased and healthy tissues. They are particularly interested in understanding the molecular mechanisms behind cellular quiescence, proliferation, and differentiation and how these fundamental cellular behaviors can be governed by microenvironmental interaction. This research focus is a culmination of his research experience to date in some of the world’s top institutions and utilizes a multidisciplinary combination of approaches, including multidimensional spatial ‘omics’ analysis, image cytometry, biomechanical characterization, flow cytometry and in vitro scaffold design in addition to standard biochemistry.
Affiliations and expertise
Lecturer in Chemical Sciences, Health Research Institute, University of Limerick – Limerick, Ireland