Single Cell Methods: Sequencing and Proteomics

Description

This volume provides a comprehensive overview for investigating biology at the level of individual cells. Chapters are organized into eight parts detailing a single-cell lab, single cell DNA-seq, RNA-seq, single cell proteomic and epigenetic, single cell multi-omics, single cell screening, and single cell live imaging. 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. Authoritative and cutting-edge, Single Cell Methods: Sequencing and Proteomics aims to make each experiment easily reproducible in every lab. Front Matter ....Pages i-xvi Front Matter ....Pages 1-1 Setting Up a Single-Cell Genomic Laboratory (Lira Mamanova)....Pages 3-8 Tissue Handling and Dissociation for Single-Cell RNA-Seq (Felipe A. Vieira Braga, Ricardo J. Miragaia)....Pages 9-21 Front Matter ....Pages 23-23 Full-Length Single-Cell RNA Sequencing with Smart-seq2 (Simone Picelli)....Pages 25-44 CEL-Seq2—Single-Cell RNA Sequencing by Multiplexed Linear Amplification (Itai Yanai, Tamar Hashimshony)....Pages 45-56 Single-Cell RNA-Seq by Multiple Annealing and Tailing-Based Quantitative Single-Cell RNA-Seq (MATQ-Seq) (Kuanwei Sheng, Chenghang Zong)....Pages 57-71 Single-Cell RNA Sequencing with Drop-Seq (Josephine Bageritz, Gianmarco Raddi)....Pages 73-85 Chromium 10× Single-Cell 3′ mRNA Sequencing of Tumor-Infiltrating Lymphocytes (Marco De Simone, Grazisa Rossetti, Massimiliano Pagani)....Pages 87-110 Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing (Toby P. Aicher, Shaina Carroll, Gianmarco Raddi, Todd Gierahn, Marc H. Wadsworth II, Travis K. Hughes et al.)....Pages 111-132 Single-Cell Tagged Reverse Transcription (STRT-Seq) (Kedar Nath Natarajan)....Pages 133-153 Single-Cell RNA-Sequencing of Peripheral Blood Mononuclear Cells with ddSEQ (Shaheen Khan, Kelly A. Kaihara)....Pages 155-176 High-Throughput Single-Cell Real-Time Quantitative PCR Analysis (Liora Haim-Vilmovsky)....Pages 177-183 Single-Cell Dosing and mRNA Sequencing of Suspension and Adherent Cells Using the PolarisTM System (Chad D. Sanada, Aik T. Ooi)....Pages 185-195 Targeted TCR Amplification from Single-Cell cDNA Libraries (Shuqiang Li, Kenneth J. Livak)....Pages 197-224 Front Matter ....Pages 225-225 Sequencing the Genomes of Single Cells (Veronica Gonzalez-Pena, Charles Gawad)....Pages 227-234 Studying DNA Methylation in Single-Cell Format with scBS-seq (Natalia Kunowska)....Pages 235-250 Single-Cell 5fC Sequencing (Chenxu Zhu, Yun Gao, Jinying Peng, Fuchou Tang, Chengqi Yi)....Pages 251-267 ChIPmentation for Low-Input Profiling of In Vivo Protein–DNA Interactions (Natalia Kunowska, Xi Chen)....Pages 269-282 Front Matter ....Pages 283-283 Immunophenotyping of Human Peripheral Blood Mononuclear Cells by Mass Cytometry (Susanne Heck, Cynthia Jane Bishop, Richard Jonathan Ellis)....Pages 285-303 Classification of the Immune Composition in the Tumor Infiltrate (Davide Brusa, Jean-Luc Balligand)....Pages 305-315 Front Matter ....Pages 317-317 Combined Genome and Transcriptome (G&T) Sequencing of Single Cells (Iraad F. Bronner, Stephan Lorenz)....Pages 319-362 Simultaneous Profiling of mRNA Transcriptome and DNA Methylome from a Single Cell (Youjin Hu, Qin An, Ying Guo, Jiawei Zhong, Shuxin Fan, Pinhong Rao et al.)....Pages 363-377 Simultaneous Targeted Detection of Proteins and RNAs in Single Cells (Aik T. Ooi, David W. Ruff)....Pages 379-392 Front Matter ....Pages 393-393 CRISPR Screening in Single Cells (Johan Henriksson)....Pages 395-406 Front Matter ....Pages 407-407 Single-Cell Live Imaging (Toru Hiratsuka, Naoki Komatsu)....Pages 409-421 Front Matter ....Pages 423-423 Differential Expression Analysis in Single-Cell Transcriptomics (Luca Alessandrì, Maddalena Arigoni, Raffaele Calogero)....Pages 425-432 A Bioinformatic Toolkit for Single-Cell mRNA Analysis (Kevin Baßler, Patrick Günther, Jonas Schulte-Schrepping, Matthias Becker, Paweł Biernat)....Pages 433-455 Back Matter ....Pages 457-459