Titlebook: Single Cell Transcriptomics; Methods and Protocol Raffaele A. Calogero,Vladimir Benes Book 2023 The Editor(s) (if applicable) and The Autho

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Full-Length Single-Cell RNA-Sequencing with FLASH-seq,377–382, 2009). While the first methods analyzed just a handful of cells, the throughput and performance rapidly increased over a very short time span. However, it was not until the introduction of emulsion droplets methods, such as the well-known kits commercialized by 10x Genomics, that the robust

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Ensuring Quality Cell Input for Single Cell Sequencing Experiments by Viability and Singlet Enrichmds. Given the sensitivity of the current methods in single cell sequencing and the minuscule amounts of RNA present within a single cell, any extrinsic source of variability should be reduced by ensuring a homogenous input right at the start. Not every tissue is as readily handled as a single cell s

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Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples), is mandatory in scRNA-seq methods, might lead to the loss of fragile cells and of spatial information, thus limiting the acquisition of the tissue cellular organization. Spatial transcriptomics methods moderate the above-mentioned issues and provide single-cell transcripts detection over an intact

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Irremediable

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Identifying Gene Markers Associated with Cell Subpopulations,bpopulation cluster. In this chapter, we describe the use of sparsely connected autoencoder, as a tool to convert single-cell clusters in pseudo-RNAseq experiments to be used as input for differential expression analysis, and the use of COMET, as a tool to depict cluster-specific gene markers.

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A Guide to Trajectory Inference and RNA Velocity,ty. Recently, significant attention has focused on investigating, from single-cell RNA-sequencing (scRNA-seq) data, cellular dynamic processes, such as cell differentiation, cell cycle and cell (de)activation. In particular, trajectory inference methods, by ordering cells along a trajectory, allow e

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Integration of scATAC-Seq with scRNA-Seq Data,tance, single-cell RNA sequencing (scRNA-Seq) measures the transcriptome-wide gene expression at a single-cell resolution, allowing for studying the heterogeneity among the cells of the same population and revealing complex and rare cell populations. On the other hand, single-cell Assay for Transpos

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