دورية أكاديمية
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Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

التفاصيل البيبلوغرافية
العنوان: Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
المؤلفون: Mimitou EP; Technology Innovation Lab, New York Genome Center, New York, NY, USA., Lareau CA; Department of Pathology, Stanford University, Stanford, CA, USA.; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology / Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., Chen KY; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.; Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan., Zorzetto-Fernandes AL; BioLegend, Inc., San Diego, CA, USA., Hao Y; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Takeshima Y; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan., Luo W; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology / Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., Huang TS; BioLegend, Inc., San Diego, CA, USA., Yeung BZ; BioLegend, Inc., San Diego, CA, USA., Papalexi E; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Thakore PI; Broad Institute of MIT and Harvard, Cambridge, MA, USA., Kibayashi T; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan., Wing JB; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.; Laboratory of Human Immunology (Single Cell Immunology), Immunology Frontier Research Center, Osaka University, Osaka, Japan., Hata M; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan., Satija R; Center for Genomics and Systems Biology, New York University, New York, NY, USA.; New York Genome Center, New York, NY, USA., Nazor KL; BioLegend, Inc., San Diego, CA, USA., Sakaguchi S; Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.; Department of Experimental Pathology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan., Ludwig LS; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology / Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.; Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany., Sankaran VG; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; Division of Hematology / Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA., Regev A; Broad Institute of MIT and Harvard, Cambridge, MA, USA.; New York Genome Center, New York, NY, USA.; Howard Hughes Medical Institute, Chevy Chase, MD, USA.; Department of Biology and Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.; Genentech, South San Francisco, CA, USA., Smibert P; Technology Innovation Lab, New York Genome Center, New York, NY, USA. smibertp@gmail.com.
المصدر: Nature biotechnology [Nat Biotechnol] 2021 Oct; Vol. 39 (10), pp. 1246-1258. Date of Electronic Publication: 2021 Jun 03.
نوع المنشور: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature America Publishing Country of Publication: United States NLM ID: 9604648 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1546-1696 (Electronic) Linking ISSN: 10870156 NLM ISO Abbreviation: Nat Biotechnol Subsets: MEDLINE
أسماء مطبوعة: Publication: New York Ny : Nature America Publishing
Original Publication: New York, NY : Nature Pub. Co., [1996-
مواضيع طبية MeSH: RNA-Seq/*methods , Single-Cell Analysis/*methods, Cell Differentiation ; Cell Lineage ; Chromatin/genetics ; Chromatin/metabolism ; DNA, Mitochondrial/genetics ; Epigenomics ; Gene Expression Profiling ; Gene Expression Regulation ; Hematopoiesis ; Humans ; Leukocytes, Mononuclear/cytology ; Leukocytes, Mononuclear/metabolism ; Proteins/genetics ; Proteins/metabolism ; T-Lymphocytes/cytology ; T-Lymphocytes/metabolism
مستخلص: Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.
(© 2021. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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معلومات مُعتمدة: RM1 HG011014 United States HG NHGRI NIH HHS; R21 HG009748 United States HG NHGRI NIH HHS; R01 HL146500 United States HL NHLBI NIH HHS; R01 DK103794 United States DK NIDDK NIH HHS; U54 DK106829 United States DK NIDDK NIH HHS
المشرفين على المادة: 0 (Chromatin)
0 (DNA, Mitochondrial)
0 (Proteins)
تواريخ الأحداث: Date Created: 20210604 Date Completed: 20211116 Latest Revision: 20240405
رمز التحديث: 20240405
مُعرف محوري في PubMed: PMC8763625
DOI: 10.1038/s41587-021-00927-2
PMID: 34083792
قاعدة البيانات: MEDLINE
الوصف
تدمد:1546-1696
DOI:10.1038/s41587-021-00927-2