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Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling

The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic pr...

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Autores principales: Sandoval, Leticia, Mohammed Ismail, Wazim, Mazzone, Amelia, Dumbrava, Mihai, Fernandez, Jenna, Munankarmy, Amik, Lasho, Terra, Binder, Moritz, Simon, Vernadette, Kim, Kwan Hyun, Chia, Nicholas, Lee, Jeong-Heon, Weroha, S. John, Patnaik, Mrinal, Gaspar-Maia, Alexandre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297939/
https://www.ncbi.nlm.nih.gov/pubmed/37372428
http://dx.doi.org/10.3390/genes14061245
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author Sandoval, Leticia
Mohammed Ismail, Wazim
Mazzone, Amelia
Dumbrava, Mihai
Fernandez, Jenna
Munankarmy, Amik
Lasho, Terra
Binder, Moritz
Simon, Vernadette
Kim, Kwan Hyun
Chia, Nicholas
Lee, Jeong-Heon
Weroha, S. John
Patnaik, Mrinal
Gaspar-Maia, Alexandre
author_facet Sandoval, Leticia
Mohammed Ismail, Wazim
Mazzone, Amelia
Dumbrava, Mihai
Fernandez, Jenna
Munankarmy, Amik
Lasho, Terra
Binder, Moritz
Simon, Vernadette
Kim, Kwan Hyun
Chia, Nicholas
Lee, Jeong-Heon
Weroha, S. John
Patnaik, Mrinal
Gaspar-Maia, Alexandre
author_sort Sandoval, Leticia
collection PubMed
description The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic profiling in various fields, there is a need for optimized and reliable nuclei isolation methods, mainly for human tissue samples. Herein we compared different nuclei isolation methods for cell suspensions, such as peripheral blood mononuclear cells (PBMC, n = 18) and a solid tumor type, ovarian cancer (OC, n = 18), derived from debulking surgery. Nuclei morphology and sequencing output parameters were used to evaluate the quality of preparation. Our results show that NP-40 detergent-based nuclei isolation yields better sequencing results than collagenase tissue dissociation for OC, significantly impacting cell type identification and analysis. Given the utility of applying such techniques to frozen samples, we also tested frozen preparation and digestion (n = 6). A paired comparison between frozen and fresh samples validated the quality of both specimens. Finally, we demonstrate the reproducibility of scRNA and snATAC + snRNA platform, by comparing the gene expression profiling of PBMC. Our results highlight how the choice of nuclei isolation methods is critical for obtaining quality data in multiomic assays. It also shows that the measurement of expression between scRNA and snRNA is comparable and effective for cell type identification.
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spelling pubmed-102979392023-06-28 Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling Sandoval, Leticia Mohammed Ismail, Wazim Mazzone, Amelia Dumbrava, Mihai Fernandez, Jenna Munankarmy, Amik Lasho, Terra Binder, Moritz Simon, Vernadette Kim, Kwan Hyun Chia, Nicholas Lee, Jeong-Heon Weroha, S. John Patnaik, Mrinal Gaspar-Maia, Alexandre Genes (Basel) Article The snATAC + snRNA platform allows epigenomic profiling of open chromatin and gene expression with single-cell resolution. The most critical assay step is to isolate high-quality nuclei to proceed with droplet-base single nuclei isolation and barcoding. With the increasing popularity of multiomic profiling in various fields, there is a need for optimized and reliable nuclei isolation methods, mainly for human tissue samples. Herein we compared different nuclei isolation methods for cell suspensions, such as peripheral blood mononuclear cells (PBMC, n = 18) and a solid tumor type, ovarian cancer (OC, n = 18), derived from debulking surgery. Nuclei morphology and sequencing output parameters were used to evaluate the quality of preparation. Our results show that NP-40 detergent-based nuclei isolation yields better sequencing results than collagenase tissue dissociation for OC, significantly impacting cell type identification and analysis. Given the utility of applying such techniques to frozen samples, we also tested frozen preparation and digestion (n = 6). A paired comparison between frozen and fresh samples validated the quality of both specimens. Finally, we demonstrate the reproducibility of scRNA and snATAC + snRNA platform, by comparing the gene expression profiling of PBMC. Our results highlight how the choice of nuclei isolation methods is critical for obtaining quality data in multiomic assays. It also shows that the measurement of expression between scRNA and snRNA is comparable and effective for cell type identification. MDPI 2023-06-10 /pmc/articles/PMC10297939/ /pubmed/37372428 http://dx.doi.org/10.3390/genes14061245 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Sandoval, Leticia
Mohammed Ismail, Wazim
Mazzone, Amelia
Dumbrava, Mihai
Fernandez, Jenna
Munankarmy, Amik
Lasho, Terra
Binder, Moritz
Simon, Vernadette
Kim, Kwan Hyun
Chia, Nicholas
Lee, Jeong-Heon
Weroha, S. John
Patnaik, Mrinal
Gaspar-Maia, Alexandre
Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title_full Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title_fullStr Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title_full_unstemmed Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title_short Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling
title_sort characterization and optimization of multiomic single-cell epigenomic profiling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297939/
https://www.ncbi.nlm.nih.gov/pubmed/37372428
http://dx.doi.org/10.3390/genes14061245
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