hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse sa...
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| Published in | Genome Biology Vol. 25; no. 1; pp. 109 - 22 |
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| Main Authors | , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
BioMed Central
26.04.2024
BMC |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. |
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| AbstractList | Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. Abstract Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. Abstract Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We develop hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining best-performing methods and demonstrate how this approach leads to the recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue. |
| ArticleNumber | 109 |
| Author | Halle, Lennard Ozols, Matiss André, Mylene Mariana Gonzales Dendrou, Calliope A Yeung, Hing-Yuen Wu, Xichen Heumos, Lukas Curion, Fabiola Theis, Fabian J Grant-Peters, Melissa Rich-Griffin, Charlotte Schiller, Herbert B |
| Author_xml | – sequence: 1 givenname: Fabiola surname: Curion fullname: Curion, Fabiola organization: Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany – sequence: 2 givenname: Xichen surname: Wu fullname: Wu, Xichen organization: Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany – sequence: 3 givenname: Lukas surname: Heumos fullname: Heumos, Lukas organization: TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany – sequence: 4 givenname: Mylene Mariana Gonzales surname: André fullname: André, Mylene Mariana Gonzales organization: Department of Mathematics, School of Computation, Information and Technology, Technical University of Munich, Garching, Germany – sequence: 5 givenname: Lennard surname: Halle fullname: Halle, Lennard organization: Institute of Computational Biology, Computational Health Center, Helmholtz Munich, Neuherberg, Germany – sequence: 6 givenname: Matiss surname: Ozols fullname: Ozols, Matiss organization: School of Cell Matrix and Regenerative Medicine, The University of Manchester, Manchester, UK – sequence: 7 givenname: Melissa surname: Grant-Peters fullname: Grant-Peters, Melissa organization: Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK – sequence: 8 givenname: Charlotte surname: Rich-Griffin fullname: Rich-Griffin, Charlotte organization: Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK – sequence: 9 givenname: Hing-Yuen surname: Yeung fullname: Yeung, Hing-Yuen organization: Nuffield Department of Medicine, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK – sequence: 10 givenname: Calliope A surname: Dendrou fullname: Dendrou, Calliope A organization: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, The Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK – sequence: 11 givenname: Herbert B surname: Schiller fullname: Schiller, Herbert B organization: Institute of Experimental Pneumology, LMU University Hospital, Ludwig-Maximilians University, Munich, Germany – sequence: 12 givenname: Fabian J orcidid: 0000-0002-2419-1943 surname: Theis fullname: Theis, Fabian J email: fabian.theis@helmholtz-muenchen.de, fabian.theis@helmholtz-muenchen.de, fabian.theis@helmholtz-muenchen.de organization: TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany. fabian.theis@helmholtz-muenchen.de |
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| Keywords | Genetic Hashing Nextflow Donor deconvolution Single-cell |
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| Snippet | Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs. Cell... Abstract Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs.... Abstract Single-cell multiplexing techniques (cell hashing and genetic multiplexing) combine multiple samples, optimizing sample processing and reducing costs.... |
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| SubjectTerms | Bar codes Brain - cytology Brain - metabolism Cell membranes Cells Donor deconvolution Experiments Genetic Genotype Genotype & phenotype Genotypes Hashing Humans Nextflow Oligonucleotides Pipelines Single-cell Single-Cell Analysis - methods Software Tagging |
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| Title | hadge: a comprehensive pipeline for donor deconvolution in single-cell studies |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/38671451 https://www.proquest.com/docview/3054211789 https://www.proquest.com/docview/3047941328/abstract/ https://doaj.org/article/42d6e98537b54ce08caa92cd642b91db |
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