Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing
Summary: Despite its rapidly increased availability for the study of complex tissue, single-cell RNA sequencing remains prohibitively expensive for large studies. Here, we present a protocol using oligonucleotide barcoding for the tagging and pooling of multiple samples from healing wounds, which ar...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | STAR Protocols |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2666166722008267 |
| _version_ | 1798005954992668672 |
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| author | Michael Januszyk Michelle Griffin Shamik Mascharak Heather E. Talbott Kellen Chen Dominic Henn Amanda F. Spielman Jennifer B.L. Parker Norah E. Liang Asha Cotterell Nicholas Guardino Deshka S. Foster Dhananjay Wagh John Coller Geoffrey C. Gurtner Derrick C. Wan Michael T. Longaker |
| author_facet | Michael Januszyk Michelle Griffin Shamik Mascharak Heather E. Talbott Kellen Chen Dominic Henn Amanda F. Spielman Jennifer B.L. Parker Norah E. Liang Asha Cotterell Nicholas Guardino Deshka S. Foster Dhananjay Wagh John Coller Geoffrey C. Gurtner Derrick C. Wan Michael T. Longaker |
| author_sort | Michael Januszyk |
| collection | DOAJ |
| description | Summary: Despite its rapidly increased availability for the study of complex tissue, single-cell RNA sequencing remains prohibitively expensive for large studies. Here, we present a protocol using oligonucleotide barcoding for the tagging and pooling of multiple samples from healing wounds, which are among the most challenging tissue types for this application. We describe steps to generate skin wounds in mice, followed by tissue harvest and oligonucleotide barcoding. This protocol is also applicable to other species including rats, pigs, and humans.For complete details on the use and execution of this protocol, please refer to Stoeckius et al. (2018),1 Galiano et al. (2004),2 and Mascharak et al. (2022).3 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| first_indexed | 2024-04-11T12:47:14Z |
| format | Article |
| id | doaj.art-2de5342d346f4c9a9e36c09ca4833ca7 |
| institution | Directory Open Access Journal |
| issn | 2666-1667 |
| language | English |
| last_indexed | 2024-04-11T12:47:14Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj.art-2de5342d346f4c9a9e36c09ca4833ca72022-12-22T04:23:18ZengElsevierSTAR Protocols2666-16672023-03-0141101946Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencingMichael Januszyk0Michelle Griffin1Shamik Mascharak2Heather E. Talbott3Kellen Chen4Dominic Henn5Amanda F. Spielman6Jennifer B.L. Parker7Norah E. Liang8Asha Cotterell9Nicholas Guardino10Deshka S. Foster11Dhananjay Wagh12John Coller13Geoffrey C. Gurtner14Derrick C. Wan15Michael T. Longaker16Hagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Corresponding authorHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAStanford Genomics Facility, Stanford University, Stanford, CA 94305, USAStanford Genomics Facility, Stanford University, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USAHagey Laboratory for Pediatric Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Corresponding authorSummary: Despite its rapidly increased availability for the study of complex tissue, single-cell RNA sequencing remains prohibitively expensive for large studies. Here, we present a protocol using oligonucleotide barcoding for the tagging and pooling of multiple samples from healing wounds, which are among the most challenging tissue types for this application. We describe steps to generate skin wounds in mice, followed by tissue harvest and oligonucleotide barcoding. This protocol is also applicable to other species including rats, pigs, and humans.For complete details on the use and execution of this protocol, please refer to Stoeckius et al. (2018),1 Galiano et al. (2004),2 and Mascharak et al. (2022).3 : 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/S2666166722008267Single CellRNAseqModel OrganismsGene Expression |
| spellingShingle | Michael Januszyk Michelle Griffin Shamik Mascharak Heather E. Talbott Kellen Chen Dominic Henn Amanda F. Spielman Jennifer B.L. Parker Norah E. Liang Asha Cotterell Nicholas Guardino Deshka S. Foster Dhananjay Wagh John Coller Geoffrey C. Gurtner Derrick C. Wan Michael T. Longaker Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing STAR Protocols Single Cell RNAseq Model Organisms Gene Expression |
| title | Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing |
| title_full | Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing |
| title_fullStr | Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing |
| title_full_unstemmed | Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing |
| title_short | Multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single-cell RNA sequencing |
| title_sort | multiplexed evaluation of mouse wound tissue using oligonucleotide barcoding with single cell rna sequencing |
| topic | Single Cell RNAseq Model Organisms Gene Expression |
| url | http://www.sciencedirect.com/science/article/pii/S2666166722008267 |
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