txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility
Abstract We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mou...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2024-03-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13059-023-03150-1 |
| _version_ | 1827310201076711424 |
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| author | Hao Zhang Ryan M. Mulqueen Natalie Iannuzo Dominique O. Farrera Francesca Polverino James J. Galligan Julie G. Ledford Andrew C. Adey Darren A. Cusanovich |
| author_facet | Hao Zhang Ryan M. Mulqueen Natalie Iannuzo Dominique O. Farrera Francesca Polverino James J. Galligan Julie G. Ledford Andrew C. Adey Darren A. Cusanovich |
| author_sort | Hao Zhang |
| collection | DOAJ |
| description | Abstract We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16−/−) model. Our study of CC16−/− nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model. |
| first_indexed | 2024-04-24T19:55:52Z |
| format | Article |
| id | doaj.art-45dac0a06c854b82a3eca3eae9b2d359 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-04-24T19:55:52Z |
| publishDate | 2024-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-45dac0a06c854b82a3eca3eae9b2d3592024-03-24T12:22:25ZengBMCGenome Biology1474-760X2024-03-0125114110.1186/s13059-023-03150-1txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibilityHao Zhang0Ryan M. Mulqueen1Natalie Iannuzo2Dominique O. Farrera3Francesca Polverino4James J. Galligan5Julie G. Ledford6Andrew C. Adey7Darren A. Cusanovich8Department of Cellular and Molecular Medicine, University of ArizonaDepartment of Molecular and Medical Genetics, Oregon Health & Science UniversityDepartment of Cellular and Molecular Medicine, University of ArizonaDepartment of Pharmacology and Toxicology, University of ArizonaAsthma & Airway Disease Research Center, University of ArizonaDepartment of Pharmacology and Toxicology, University of ArizonaDepartment of Cellular and Molecular Medicine, University of ArizonaDepartment of Molecular and Medical Genetics, Oregon Health & Science UniversityDepartment of Cellular and Molecular Medicine, University of ArizonaAbstract We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10× Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16−/−) model. Our study of CC16−/− nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.https://doi.org/10.1186/s13059-023-03150-1Single-cellATAC-seqChromatin accessibilityCombinatorial indexingMolecular hashingCC16 |
| spellingShingle | Hao Zhang Ryan M. Mulqueen Natalie Iannuzo Dominique O. Farrera Francesca Polverino James J. Galligan Julie G. Ledford Andrew C. Adey Darren A. Cusanovich txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility Genome Biology Single-cell ATAC-seq Chromatin accessibility Combinatorial indexing Molecular hashing CC16 |
| title | txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| title_full | txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| title_fullStr | txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| title_full_unstemmed | txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| title_short | txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| title_sort | txci atac seq a massive scale single cell technique to profile chromatin accessibility |
| topic | Single-cell ATAC-seq Chromatin accessibility Combinatorial indexing Molecular hashing CC16 |
| url | https://doi.org/10.1186/s13059-023-03150-1 |
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