High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids
Summary: Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to incre...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-09-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672200435X |
| _version_ | 1817995294223106048 |
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| author | Santiago Cerrizuela Oguzhan Kaya Lukas P.M. Kremer Andrea Sarvari Tobias Ellinger Jannes Straub Jan Brunken Andrés Sanz-Morejón Aylin Korkmaz Ana Martín-Villalba |
| author_facet | Santiago Cerrizuela Oguzhan Kaya Lukas P.M. Kremer Andrea Sarvari Tobias Ellinger Jannes Straub Jan Brunken Andrés Sanz-Morejón Aylin Korkmaz Ana Martín-Villalba |
| author_sort | Santiago Cerrizuela |
| collection | DOAJ |
| description | Summary: Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain higher numbers of detected genes and genomic DNA (gDNA) CpGs per cell. We outline normalization steps to optimally distribute per-cell sequencing depth.For complete details on the use and execution of this protocol, please refer to Clark (2019), Clark et al. (2018), and Hagemann-Jensen et al. (2020a, 2020b). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-14T02:03:54Z |
| format | Article |
| id | doaj.art-b68abcc8086c42eab66cbb022724aecb |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-14T02:03:54Z |
| publishDate | 2022-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-b68abcc8086c42eab66cbb022724aecb2022-12-22T02:18:45ZengElsevierSTAR Protocols2666-16672022-09-0133101555High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoidsSantiago Cerrizuela0Oguzhan Kaya1Lukas P.M. Kremer2Andrea Sarvari3Tobias Ellinger4Jannes Straub5Jan Brunken6Andrés Sanz-Morejón7Aylin Korkmaz8Ana Martín-Villalba9Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Corresponding authorMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, GermanyMolecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Corresponding authorSummary: Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain higher numbers of detected genes and genomic DNA (gDNA) CpGs per cell. We outline normalization steps to optimally distribute per-cell sequencing depth.For complete details on the use and execution of this protocol, please refer to Clark (2019), Clark et al. (2018), and Hagemann-Jensen et al. (2020a, 2020b). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S266616672200435XBioinformaticsSequence analysisCell BiologySingle CellGenomicsSequencing |
| spellingShingle | Santiago Cerrizuela Oguzhan Kaya Lukas P.M. Kremer Andrea Sarvari Tobias Ellinger Jannes Straub Jan Brunken Andrés Sanz-Morejón Aylin Korkmaz Ana Martín-Villalba High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids STAR Protocols Bioinformatics Sequence analysis Cell Biology Single Cell Genomics Sequencing |
| title | High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| title_full | High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| title_fullStr | High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| title_full_unstemmed | High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| title_short | High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| title_sort | high throughput scnmt protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids |
| topic | Bioinformatics Sequence analysis Cell Biology Single Cell Genomics Sequencing |
| url | http://www.sciencedirect.com/science/article/pii/S266616672200435X |
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