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Evaluation of genet...
Evaluation of genetic demultiplexing of single-cell sequencing data from model species
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- Cardiello, Joseph F (författare)
- Lund University,Lunds universitet,Avdelningen för molekylärmedicin och genterapi,Institutionen för laboratoriemedicin,Medicinska fakulteten,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,WCMM- Wallenberg center för molekylär medicinsk forskning,Regenerativ immunologi,Forskargrupper vid Lunds universitet,Division of Molecular Medicine and Gene Therapy,Department of Laboratory Medicine,Faculty of Medicine,Stem Cell Center,Division of stem cell research,WCMM-Wallenberg Centre for Molecular Medicine,Regenerative Immunology,Lund University Research Groups
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- Joven Araus, Alberto (författare)
- Karolinska Institutet,Karolinska Institute
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- Giatrellis, Sarantis (författare)
- Karolinska Institutet,Karolinska Institute
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- Helsens, Clement (författare)
- Swiss Federal Institute of Technology
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- Simon, András (författare)
- Karolinska Institutet,Karolinska Institute
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- Leigh, Nicholas D (författare)
- Lund University,Lunds universitet,Avdelningen för molekylärmedicin och genterapi,Institutionen för laboratoriemedicin,Medicinska fakulteten,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,WCMM- Wallenberg center för molekylär medicinsk forskning,Regenerativ immunologi,Forskargrupper vid Lunds universitet,Division of Molecular Medicine and Gene Therapy,Department of Laboratory Medicine,Faculty of Medicine,Stem Cell Center,Division of stem cell research,WCMM-Wallenberg Centre for Molecular Medicine,Regenerative Immunology,Lund University Research Groups
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(creator_code:org_t)
- 2023
- 2023
- Engelska.
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Ingår i: Life Science Alliance. - 2575-1077. ; 6:8
- Relaterad länk:
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http://dx.doi.org/10... (free)
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https://lup.lub.lu.s...
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https://doi.org/10.2...
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http://kipublication...
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Abstract
Ämnesord
Stäng
- Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address these problems is pooling cells from multiple individuals into one sc-seq library. In humans, genotype-based computational separation (i.e., demultiplexing) of pooled sc-seq samples is common. This approach would be instrumental for studying non-isogenic model organisms. We set out to determine whether genotype-based demultiplexing could be more broadly applied among species ranging from zebrafish to non-human primates. Using such non-isogenic species, we benchmark genotype-based demultiplexing of pooled sc-seq datasets against various ground truths. We demonstrate that genotype-based demultiplexing of pooled sc-seq samples can be used with confidence in several non-isogenic model organisms and uncover limitations of this method. Importantly, the only genomic resource required for this approach is sc-seq data and a de novo transcriptome. The incorporation of pooling into sc-seq study designs will decrease cost while simultaneously increasing the reproducibility and experimental options in non-isogenic model organisms.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- Animals
- Single cell RNA sequencing
- Reproducibility of Results
- Zebrafish/genetics
- Transcriptome
- Genomics/methods
- Sequence Analysis, RNA/methods
- demultiplexing
- regeneration model
- Developmental biology
Publikations- och innehållstyp
- art (ämneskategori)
- ref (ämneskategori)
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