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Single Cell Transcriptomics

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Raffaele A. Calogero

    1. Molecular Biotechnology Center, University of Torino, Torino, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. Vladimir Benes

    1. European Molecular Biology Laboratory, Heidelberg, Germany

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2584)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Guidance on Processing the 10x Genomics Single Cell Gene Expression Assay

    • Katharina Danielski
    Pages 1-28

  3. BD Rhapsody™ Single-Cell Analysis System Workflow: From Sample to Multimodal Single-Cell Sequencing Data

    • Jannes Ulbrich, Vadir Lopez-Salmeron, Ian Gerrard
    Pages 29-56

  4. Profiling Transcriptional Heterogeneity with Seq-Well S3: A Low-Cost, Portable, High-Fidelity Platform for Massively Parallel Single-Cell RNA-Seq

    • Riley S. Drake, Martin Arreola Villanueva, Mike Vilme, Daniela D. Russo, Andrew Navia, J. Christopher Love et al.
    Pages 57-104

  5. A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria

    • Christina Homberger, Antoine-Emmanuel Saliba, Jörg Vogel
    Pages 105-121

  6. Full-Length Single-Cell RNA-Sequencing with FLASH-seq

    • Vincent Hahaut, Simone Picelli
    Pages 123-164

  7. Plant Single-Cell/Nucleus RNA-seq Workflow

    • Sandra Thibivilliers, Andrew Farmer, Susan Schroeder, Marc Libault
    Pages 165-181

  8. Ensuring Quality Cell Input for Single Cell Sequencing Experiments by Viability and Singlet Enrichment Using Cell Sorting

    • Malte Paulsen
    Pages 183-189

  9. Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples)

    • Federica Antico, Marta Gai, Maddalena Arigoni
    Pages 191-203

  10. Single-Cell RNAseq Data QC and Preprocessing

    • Martina Olivero, Raffaele A. Calogero
    Pages 205-215

  11. Single-Cell RNAseq Complexity Reduction

    • Francesca Cordero, Raffaele A. Calogero
    Pages 217-230

  12. Functional-Feature-Based Data Reduction Using Sparsely Connected Autoencoders

    • Luca Alessandri, Raffaele A. Calogero
    Pages 231-240

  13. Single-Cell RNAseq Clustering

    • Marco Beccuti, Raffaele A. Calogero
    Pages 241-250

  14. Identifying Gene Markers Associated with Cell Subpopulations

    • Maria Luisa Ratto, Luca Alessandri
    Pages 251-268

  15. A Guide to Trajectory Inference and RNA Velocity

    • Philipp Weiler, Koen Van den Berge, Kelly Street, Simone Tiberi
    Pages 269-292

  16. Integration of scATAC-Seq with scRNA-Seq Data

    • Ivan Berest, Andrea Tangherloni
    Pages 293-310

  17. Using “Galaxy-rCASC”: A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis

    • Pietro Mandreoli, Luca Alessandri, Raffaele A. Calogero, Marco Antonio Tangaro, Federico Zambelli
    Pages 311-335

  18. Bringing Cell Subpopulation Discovery on a Cloud-HPC Using rCASC and StreamFlow

    • Sandro G. Contaldo, Luca Alessandri, Iacopo Colonnelli, Marco Beccuti, Marco Aldinucci
    Pages 337-345

  19. Profiling RNA Editing in Single Cells

    • Adriano Fonzino, Graziano Pesole, Ernesto Picardi
    Pages 347-370

  20. Practical Considerations for Complex Tissue Dissociation for Single-Cell Transcriptomics

    • Stephanie T. Pohl, Maria Llamazares Prada, Elisa Espinet, Renata Jurkowska
    Pages 371-387
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Keywords

About this book

This volume provides up-to-date methods on single cell wet and bioinformatics protocols based on the researcher experiment requirements. Chapters detail basic analytical procedures, single-cell data QC, dimensionality reduction, clustering, cluster-specific features selection, RNA velocity, multi-modal data integration, and single cell RNA editing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Single Cell Transcriptomics: Methods and Protocols aims to be a valuable resource for all researchers interested in learning more about this important and developing field.

Editors and Affiliations

  • Molecular Biotechnology Center, University of Torino, Torino, Italy

    Raffaele A. Calogero

  • European Molecular Biology Laboratory, Heidelberg, Germany

    Vladimir Benes

Bibliographic Information

  • Book Title: Single Cell Transcriptomics

  • Book Subtitle: Methods and Protocols

  • Editors: Raffaele A. Calogero, Vladimir Benes

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2756-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2755-6Published: 11 December 2022

  • Softcover ISBN: 978-1-0716-2758-7Published: 11 December 2023

  • eBook ISBN: 978-1-0716-2756-3Published: 10 December 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 390

  • Number of Illustrations: 5 b/w illustrations, 121 illustrations in colour

  • Topics: Cell Biology, Bioinformatics

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