Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis
Summary: High cell viability and recovered cell concentration are typical quality control requirements for single-cell processing and quality data. This protocol describes procedures for sampling, live-cell biobanking, preprocessing for single-cell RNA sequencing, and analysis of fine-needle aspirat...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2021-06-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166721002884 |
| _version_ | 1830308126236082176 |
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| author | Aizhan Tastanova Egle Ramelyte Zsolt Balázs Ulrike Menzel Christian Beisel Michael Krauthammer Reinhard Dummer Mitchell Paul Levesque |
| author_facet | Aizhan Tastanova Egle Ramelyte Zsolt Balázs Ulrike Menzel Christian Beisel Michael Krauthammer Reinhard Dummer Mitchell Paul Levesque |
| author_sort | Aizhan Tastanova |
| collection | DOAJ |
| description | Summary: High cell viability and recovered cell concentration are typical quality control requirements for single-cell processing and quality data. This protocol describes procedures for sampling, live-cell biobanking, preprocessing for single-cell RNA sequencing, and analysis of fine-needle aspiration (FNA) samples of the skin. The minimally invasive nature of FNA collection is more accepted by patients and allows for frequent longitudinal sampling, resulting in high-quality single-cell sequencing data that capture cellular heterogeneity in clinical samples. |
| first_indexed | 2024-12-19T10:43:57Z |
| format | Article |
| id | doaj.art-572c00d3885c431f9a1fad751341172a |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-12-19T10:43:57Z |
| publishDate | 2021-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-572c00d3885c431f9a1fad751341172a2022-12-21T20:25:20ZengElsevierSTAR Protocols2666-16672021-06-0122100581Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysisAizhan Tastanova0Egle Ramelyte1Zsolt Balázs2Ulrike Menzel3Christian Beisel4Michael Krauthammer5Reinhard Dummer6Mitchell Paul Levesque7Dermatology Department, University Hospital Zurich and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; Corresponding authorDermatology Department, University Hospital Zurich and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; Corresponding authorDepartment of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland; Biomedical Informatics, University Hospital of Zurich, 8057 Zurich, Switzerland; Corresponding authorDepartment of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, SwitzerlandDepartment of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, SwitzerlandDepartment of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland; Biomedical Informatics, University Hospital of Zurich, 8057 Zurich, SwitzerlandDermatology Department, University Hospital Zurich and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; Corresponding authorDermatology Department, University Hospital Zurich and Medical Faculty, University of Zurich, 8091 Zurich, Switzerland; Corresponding authorSummary: High cell viability and recovered cell concentration are typical quality control requirements for single-cell processing and quality data. This protocol describes procedures for sampling, live-cell biobanking, preprocessing for single-cell RNA sequencing, and analysis of fine-needle aspiration (FNA) samples of the skin. The minimally invasive nature of FNA collection is more accepted by patients and allows for frequent longitudinal sampling, resulting in high-quality single-cell sequencing data that capture cellular heterogeneity in clinical samples.http://www.sciencedirect.com/science/article/pii/S2666166721002884BioinformaticsCell isolationSingle CellClinical ProtocolRNAseq |
| spellingShingle | Aizhan Tastanova Egle Ramelyte Zsolt Balázs Ulrike Menzel Christian Beisel Michael Krauthammer Reinhard Dummer Mitchell Paul Levesque Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis STAR Protocols Bioinformatics Cell isolation Single Cell Clinical Protocol RNAseq |
| title | Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| title_full | Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| title_fullStr | Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| title_full_unstemmed | Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| title_short | Collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| title_sort | collection and preprocessing of fine needle aspirate patient samples for single cell profiling and data analysis |
| topic | Bioinformatics Cell isolation Single Cell Clinical Protocol RNAseq |
| url | http://www.sciencedirect.com/science/article/pii/S2666166721002884 |
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