We are analyzing https://link.springer.com/article/10.1186/s13059-018-1603-1.

Title:
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics | Genome Biology
Description:
Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and “super-load” commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.
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Keywords {🔍}

cell, cells, hto, antibodies, barcodes, hashing, single, based, sample, fig, data, article, multiplexing, rna, negative, singlecell, multiplets, singlets, classified, demuxlet, google, scholar, genomics, expression, citeseq, antibody, methods, sequencing, samples, umi, adt, usa, expressed, hekt, highly, scrnaseq, levels, additional, file, experiment, counts, classification, performed, surface, human, htos, observed, positive, concentrations, cas,

Topics {✒️}

high-throughput drug screening $$ \mathrm{si}=\frac{{\mathrm{pos}}_{0 single-cell rna-seq reveals multiplexed single-cell rna-seq scaling single-cell genomics 5}}{2\times \mathrm{mad}\left single-cell rna-sequencing experiments sodium-potassium atpase-subunit trans-cyclooctene-peg4-acid hg19-mm10 concatenated reference single-stranded polya oligos single-cell rna-seq data-driven phenotypic dissection commercial droplet-based systems trans-cyclooctene-peg4-nhs gov/geo/query/acc single-cell rna sequencing single-cell transcriptome resolution cell isolation methyltetrazine-peg4-nhs ester commercial scrna-seq platforms measured alongside scrna-seq single scrna-seq experiment single-cell transcriptomics applied antibody-oligo conjugates provided single cell genomics low-resolution pre-clustering ubiquitous surface proteins standard scrna-seq protocols cite-seq antibody panels antibody-oligo conjugation protocols cite-seq immunophenotyping antibodies biasing scrna-seq results drop-seq tools v1 predicted cell-type expression initial k-medoids clustering 10x genomics instrument standard drop-seq pipeline discriminating low-quality cells article download pdf cell surface proteins /hoohm/cite-seq-count 10x chromium instrument 10x genomics libraries recover low-quality cells full size image york genome center sample-specific batch effects immune system high dimensional data

Questions {❓}

Schema {🗺️}

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         headline:Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
         description:Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and “super-load” commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.
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         dateModified:2018-12-19T00:00:00Z
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            Evolutionary Biology
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      headline:Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
      description:Despite rapid developments in single cell sequencing, sample-specific batch effects, detection of cell multiplets, and experimental costs remain outstanding challenges. Here, we introduce Cell Hashing, where oligo-tagged antibodies against ubiquitously expressed surface proteins uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its original sample, robustly identify cross-sample multiplets, and “super-load” commercial droplet-based systems for significant cost reduction. We validate our approach using a complementary genetic approach and demonstrate how hashing can generalize the benefits of single cell multiplexing to diverse samples and experimental designs.
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         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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               type:PostalAddress
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            name:BioLegend Inc.
            address:
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               type:PostalAddress
            type:Organization
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      affiliation:
            name:New York Genome Center
            address:
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               type:PostalAddress
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      name:Technology Innovation Lab, New York Genome Center, New York, USA
      name:NYU Center for Genomics and Systems Biology, New York Genome Center, New York, USA

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