A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid Article Swipe
Hanane Touil
,
Tina Roostaei
,
Daniela Calini
,
Claudiu Diaconu
,
Samantha Epstein
,
Catarina Raposo
,
Kaho Onomichi
,
Kiran T. Thakur
,
Licínio Craveiro
,
Ilaria Callegari
,
Julien Bryois
,
Claire Riley
,
Vilas Menon
,
Tobias Derfuß
,
Philip L. De Jager
,
Dheeraj Malhotra
·
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.crmeth.2023.100533
YOU?
·
· 2023
· Open Access
·
· DOI: https://doi.org/10.1016/j.crmeth.2023.100533
Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an unprecedented level. Here, we report a robust cryopreservation protocol adapted for the characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate- to large-scale studies. Fresh CSF was collected from twenty-one participants at two independent sites. Each CSF sample was split into two fractions: one was processed fresh, while the second was cryopreserved for months and profiled after thawing. B and T cell receptor sequencing was also performed. Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. We find no significant difference in cell type proportions and cellular transcriptomes between fresh and cryopreserved cells. Results were comparable at both sites and with different single-cell sequencing chemistries. Cryopreservation did not affect recovery of T and B cell clonotype diversity. Our CSF cell cryopreservation protocol provides an important alternative to fresh processing of fragile CSF cells.
Related Topics
Concepts
Cryopreservation
Transcriptome
Cell
Cerebrospinal fluid
Biology
Andrology
Deep sequencing
Cell biology
Molecular biology
Embryo
Genetics
Gene
Gene expression
Medicine
Genome
Neuroscience
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1016/j.crmeth.2023.100533
- OA Status
- gold
- Cited By
- 14
- References
- 22
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4384301782
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4384301782Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1016/j.crmeth.2023.100533Digital Object Identifier
- Title
-
A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluidWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2023Year of publication
- Publication date
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2023-07-01Full publication date if available
- Authors
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Hanane Touil, Tina Roostaei, Daniela Calini, Claudiu Diaconu, Samantha Epstein, Catarina Raposo, Kaho Onomichi, Kiran T. Thakur, Licínio Craveiro, Ilaria Callegari, Julien Bryois, Claire Riley, Vilas Menon, Tobias Derfuß, Philip L. De Jager, Dheeraj MalhotraList of authors in order
- Landing page
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https://doi.org/10.1016/j.crmeth.2023.100533Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://doi.org/10.1016/j.crmeth.2023.100533Direct OA link when available
- Concepts
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Cryopreservation, Transcriptome, Cell, Cerebrospinal fluid, Biology, Andrology, Deep sequencing, Cell biology, Molecular biology, Embryo, Genetics, Gene, Gene expression, Medicine, Genome, NeuroscienceTop concepts (fields/topics) attached by OpenAlex
- Cited by
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14Total citation count in OpenAlex
- Citations by year (recent)
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2025: 7, 2024: 6, 2023: 1Per-year citation counts (last 5 years)
- References (count)
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22Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| abstract_inverted_index.CSF | 26, 39, 50, 99, 144, 157 |
| abstract_inverted_index.Our | 81, 143 |
| abstract_inverted_index.RNA | 30 |
| abstract_inverted_index.all | 97 |
| abstract_inverted_index.and | 68, 73, 85, 111, 116, 125, 138 |
| abstract_inverted_index.did | 132 |
| abstract_inverted_index.for | 21, 66 |
| abstract_inverted_index.not | 133 |
| abstract_inverted_index.one | 57 |
| abstract_inverted_index.the | 22, 62, 89 |
| abstract_inverted_index.two | 46, 55 |
| abstract_inverted_index.was | 40, 52, 58, 64, 78 |
| abstract_inverted_index.Each | 49 |
| abstract_inverted_index.also | 79 |
| abstract_inverted_index.both | 123 |
| abstract_inverted_index.cell | 75, 100, 108, 140, 145 |
| abstract_inverted_index.data | 87 |
| abstract_inverted_index.find | 103 |
| abstract_inverted_index.from | 42, 88 |
| abstract_inverted_index.into | 54 |
| abstract_inverted_index.same | 90 |
| abstract_inverted_index.type | 109 |
| abstract_inverted_index.were | 120 |
| abstract_inverted_index.with | 126 |
| abstract_inverted_index.(CSF) | 7 |
| abstract_inverted_index.Fresh | 38 |
| abstract_inverted_index.Here, | 13 |
| abstract_inverted_index.after | 70 |
| abstract_inverted_index.cells | 8, 27 |
| abstract_inverted_index.fluid | 6 |
| abstract_inverted_index.fresh | 84, 115, 153 |
| abstract_inverted_index.known | 98 |
| abstract_inverted_index.sites | 124 |
| abstract_inverted_index.split | 53 |
| abstract_inverted_index.while | 61 |
| abstract_inverted_index.affect | 134 |
| abstract_inverted_index.allows | 2 |
| abstract_inverted_index.cells. | 118, 158 |
| abstract_inverted_index.fresh, | 60 |
| abstract_inverted_index.highly | 93 |
| abstract_inverted_index.level. | 12 |
| abstract_inverted_index.months | 67 |
| abstract_inverted_index.report | 15 |
| abstract_inverted_index.robust | 17 |
| abstract_inverted_index.sample | 51 |
| abstract_inverted_index.second | 63 |
| abstract_inverted_index.sites. | 48 |
| abstract_inverted_index.types. | 101 |
| abstract_inverted_index.Results | 119 |
| abstract_inverted_index.adapted | 20 |
| abstract_inverted_index.between | 114 |
| abstract_inverted_index.fragile | 25, 156 |
| abstract_inverted_index.cellular | 112 |
| abstract_inverted_index.profiled | 69 |
| abstract_inverted_index.protocol | 19, 147 |
| abstract_inverted_index.provides | 148 |
| abstract_inverted_index.receptor | 76 |
| abstract_inverted_index.recovery | 95, 135 |
| abstract_inverted_index.studies. | 37 |
| abstract_inverted_index.thawing. | 71 |
| abstract_inverted_index.(RNA-seq) | 32 |
| abstract_inverted_index.clonotype | 141 |
| abstract_inverted_index.collected | 41 |
| abstract_inverted_index.different | 127 |
| abstract_inverted_index.efficient | 94 |
| abstract_inverted_index.important | 150 |
| abstract_inverted_index.moderate- | 34 |
| abstract_inverted_index.processed | 59 |
| abstract_inverted_index.comparable | 121 |
| abstract_inverted_index.comparison | 82 |
| abstract_inverted_index.difference | 106 |
| abstract_inverted_index.diversity. | 142 |
| abstract_inverted_index.fractions: | 56 |
| abstract_inverted_index.performed. | 80 |
| abstract_inverted_index.processing | 154 |
| abstract_inverted_index.sequencing | 31, 77, 129 |
| abstract_inverted_index.twenty-one | 43 |
| abstract_inverted_index.Single-cell | 0 |
| abstract_inverted_index.alternative | 151 |
| abstract_inverted_index.independent | 47 |
| abstract_inverted_index.individuals | 91 |
| abstract_inverted_index.large-scale | 36 |
| abstract_inverted_index.proportions | 110 |
| abstract_inverted_index.significant | 105 |
| abstract_inverted_index.single-cell | 29, 128 |
| abstract_inverted_index.chemistries. | 130 |
| abstract_inverted_index.demonstrates | 92 |
| abstract_inverted_index.participants | 44 |
| abstract_inverted_index.cerebrospinal | 5 |
| abstract_inverted_index.cryopreserved | 65, 86, 117 |
| abstract_inverted_index.unprecedented | 11 |
| abstract_inverted_index.transcriptomes | 113 |
| abstract_inverted_index.transcriptomics | 1 |
| abstract_inverted_index.Cryopreservation | 131 |
| abstract_inverted_index.characterization | 3, 23 |
| abstract_inverted_index.cryopreservation | 18, 146 |
| cited_by_percentile_year.max | 99 |
| cited_by_percentile_year.min | 89 |
| corresponding_author_ids | https://openalex.org/A5103029658, https://openalex.org/A5049324919 |
| countries_distinct_count | 2 |
| institutions_distinct_count | 16 |
| corresponding_institution_ids | https://openalex.org/I118019719, https://openalex.org/I1297540436, https://openalex.org/I2799503643 |
| citation_normalized_percentile.value | 0.91299564 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | True |