Dual-Indexed Sequencing Run: Single Cell 5' v2 Dual Index V(D)J libraries are dual-indexed. We do not recommend sequencing 10x Single Cell 5' v2 Dual Index V(D)J libraries with a single-index configuration. ReadRead 1i7 Indexi5 IndexRead 2 Purpose 10x™ Barcode, UMI...
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a Schematic of intra-tumor lymphocytes identified from single-cell V(D)J sequencing on the 10× platform. b Identification of two presumed clonotypes composed of five and four barcodes. These clonotypes are likely to have been derived from one cell observed multiple times via barcode multiplets...
Extensive genomic and transcriptomic heterogeneity in human cancer often negatively impacts treatment efficacy and survival, thus posing a significant ongoing challenge for modern treatment regimens. State-of-the-art DNA- and RNA-sequencing methods now p
Sequence at lower depth if large savings on sequencing cost are more important than modest increases to yield. Combining V(D)J data from one library sequenced across multiple lanes or flow cells Reads from a library that was sequenced across multiple flow cells can be pooled. Follow the steps...
Single-cell sequencing provides detailed insights into biological processes including cell differentiation and identity. While providing deep cell-specific information, the method suffers from technical constraints, most notably a limited number of expressed genes per cell, which leads to suboptimal clustering...
The application of single-cell RNA sequencing (scRNA-seq) in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies. With the expansion of capacity f
All scRNA sequencing datasets were quality control filtered according to read depth and distributions of counts. Following empty droplet and doublet removal, dying cells were removed by ensuring less than 20% of total reads were mapped to mitochondrial transcripts. Genes were filtered out if they we...
specificity of gene expression quantifications, leading to rapid progress in single-cell transcriptome profiling methods. In this chapter, we provide a timely review on basic principles of single-cell RNA sequencing methods and discuss the technical challenges and their applications in research and ...
Figure 1. Single-Cell RNA Sequencing Establishes Germ and Somatic Cell Types Residing within the Cynomolgus Testis (A) Schematic of the experimental design. (B) t-SNE of scRNA-seq data comprising 16,932 cells (cells are colored by the 11 broad cell types). (C) (Ci) Heatmap showing expre...