Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells
Abstract The main critical step in single-cell transcriptomics is sample preparation. Several methods have been developed to preserve cells after dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the cell types to be processed. In thi...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-05-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-023-04834-x |
| _version_ | 1797801283505094656 |
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| author | Ana Gutiérrez-Franco Franz Ake Mohamed N. Hassan Natalie Chaves Cayuela Loris Mularoni Mireya Plass |
| author_facet | Ana Gutiérrez-Franco Franz Ake Mohamed N. Hassan Natalie Chaves Cayuela Loris Mularoni Mireya Plass |
| author_sort | Ana Gutiérrez-Franco |
| collection | DOAJ |
| description | Abstract The main critical step in single-cell transcriptomics is sample preparation. Several methods have been developed to preserve cells after dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the cell types to be processed. In this project, we perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq on neural and glial cells derived from induced pluripotent stem cells. Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell, it strongly affects the cellular composition and induces the expression of stress and apoptosis genes. In contrast, methanol fixed samples display a cellular composition similar to fresh samples and provide a good cell quality and little expression biases. Taken together, our results show that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations. |
| first_indexed | 2024-03-13T04:48:06Z |
| format | Article |
| id | doaj.art-0e2bf38c8a3748cf955996eacd5a1a07 |
| institution | Directory Open Access Journal |
| issn | 2399-3642 |
| language | English |
| last_indexed | 2024-03-13T04:48:06Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj.art-0e2bf38c8a3748cf955996eacd5a1a072023-06-18T11:22:19ZengNature PortfolioCommunications Biology2399-36422023-05-016111210.1038/s42003-023-04834-xMethanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cellsAna Gutiérrez-Franco0Franz Ake1Mohamed N. Hassan2Natalie Chaves Cayuela3Loris Mularoni4Mireya Plass5Gene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del LlobregatGene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del LlobregatGene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del LlobregatGene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del LlobregatProgram for Advancing Clinical Translation of Regenerative Medicine of Catalonia, P-CMR[C], L’Hospitalet del LlobregatGene Regulation of Cell Identity, Regenerative Medicine Program, Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet del LlobregatAbstract The main critical step in single-cell transcriptomics is sample preparation. Several methods have been developed to preserve cells after dissociation to uncouple sample handling from library preparation. Yet, the suitability of these methods depends on the cell types to be processed. In this project, we perform a systematic comparison of preservation methods for droplet-based single-cell RNA-seq on neural and glial cells derived from induced pluripotent stem cells. Our results show that while DMSO provides the highest cell quality in terms of RNA molecules and genes detected per cell, it strongly affects the cellular composition and induces the expression of stress and apoptosis genes. In contrast, methanol fixed samples display a cellular composition similar to fresh samples and provide a good cell quality and little expression biases. Taken together, our results show that methanol fixation is the method of choice for performing droplet-based single-cell transcriptomics experiments on neural cell populations.https://doi.org/10.1038/s42003-023-04834-x |
| spellingShingle | Ana Gutiérrez-Franco Franz Ake Mohamed N. Hassan Natalie Chaves Cayuela Loris Mularoni Mireya Plass Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells Communications Biology |
| title | Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells |
| title_full | Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells |
| title_fullStr | Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells |
| title_full_unstemmed | Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells |
| title_short | Methanol fixation is the method of choice for droplet-based single-cell transcriptomics of neural cells |
| title_sort | methanol fixation is the method of choice for droplet based single cell transcriptomics of neural cells |
| url | https://doi.org/10.1038/s42003-023-04834-x |
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