8/31/2023 0 Comments 10x chromium system![]() ![]() Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-seq. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response. Pooled CRISPR screening with single-cell transcriptome readout. The Human Tumor Atlas Network: charting tumor transitions across space and time at single-cell resolution. Single-cell sequencing-based technologies will revolutionize whole-organism science. Massively multiplex chemical transcriptomics at single-cell resolution. Quantitation of mRNA transcripts and proteins using the BD Rhapsody single-cell analysis system. Construction of a human cell landscape at single-cell level. ![]() Mapping the mouse cell atlas by Microwell-seq. Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. Combinatorial labeling of single cells for gene expression cytometry. The single-cell transcriptional landscape of mammalian organogenesis. Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding. Comprehensive single-cell transcriptional profiling of a multicellular organism. Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes. ![]() Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. CellTag Indexing: genetic barcode-based sample multiplexing for single-cell genomics. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. ![]() Massively parallel digital transcriptional profiling of single cells. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. We benchmarked scifi-RNA-seq on various human and mouse cell lines, validated it for primary human T cells and applied it in a highly multiplexed CRISPR screen with single-cell transcriptome readout of T cell receptor activation. Compared to cell hashing methods, which flag and discard droplets containing more than one cell, scifi-RNA-seq resolves and retains individual transcriptomes from overloaded droplets. Compared with multiround combinatorial indexing, scifi-RNA-seq provides an easy and efficient workflow. Thereby, scifi-RNA-seq massively increases the throughput of droplet-based single-cell RNA-seq, and provides a straightforward way of multiplexing thousands of samples in a single experiment. Preindexing allows us to load several cells per droplet and computationally demultiplex their individual expression profiles. The scifi-RNA-seq assay combines one-step combinatorial preindexing of entire transcriptomes inside permeabilized cells with subsequent single-cell RNA-seq using microfluidics. To enable cost-effective single-cell sequencing for millions of individual cells, we developed ‘single-cell combinatorial fluidic indexing’ (scifi). Cell atlas projects and high-throughput perturbation screens require single-cell sequencing at a scale that is challenging with current technology. ![]()
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