Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Baron, Chloé S.; Barve, Aditya; Muraro, Mauro J.; Linden, Reinier van der; Dharmadhikari, Gitanjali; Lyubimova, Anna; Koning, Eelco J.P. de; Oudenaarden, Alexander van

doi:10.1016/j.cell.2019.08.006

Cited by 53 publications

(55 citation statements)

References 62 publications

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“…The resulting t-SNE map highlighted particular cell types, in line with recent scRNA-seq studies of hematopoietic organs of zebrafish 43–50 , which expressed validated hematopoietic lineage markers (Table S1). Cells in cluster 2 and 4 expressed HSPC-related genes, such as gata2b, gfi1aa, meis1b, myb and pmp22b, consistent with expression in mammalian HSCs and zebrafish HSPCs 44–48,50 (Figure 5a,b). RaceID3 subdivided the main HSPC cluster into two, HSPCs I and HSPCs II, based on ENSDARG00000080337_ACO24175.4 and tmed1b .…”

Section: Resultssupporting

confidence: 64%

Phosphatidylinositol-3 kinase activity controls survival and stemness of zebrafish hematopoietic stem/progenitor cells

Blokzijl-Franke

Ponsioen

Schulte‐Merker

et al. 2020

Preprint

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Hematopoietic Stem and Progenitor Cells (HSPCs) are multipotent cells giving rise to all blood lineages during life. HSPCs emerge from the ventral wall of the dorsal aorta (VDA) during a specific timespan in embryonic development through endothelial hematopoietic transition (EHT). We investigated the ontogeny of HSPCs in mutant zebrafish embryos lacking functional pten, an important tumor suppressor with a central role in cell signaling. Through in vivo live imaging, we discovered that in pten mutant embryos a proportion of the HSPCs died upon emergence from the VDA, an effect rescued by inhibition of phosphatidylinositol-3 kinase (PI3K). Surprisingly, inhibition of PI3K in wild type embryos also induced HSPC death. Surviving HSPCs colonized the caudal hematopoietic tissue (CHT) normally and committed to all blood lineages. Single cell RNA sequencing indicated that inhibition of PI3K enhanced survival of multi-potent progenitors , whereas the number of HSPCs with more stem-like properties was reduced. At the end of the definitive wave, loss of Pten caused a shift to more restricted progenitors at the expense of HSPCs. We conclude that PI3K signaling tightly controls HSPCs survival and both up- and downregulation of PI3K signaling reduces stemness of HSPCs.

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Section: Resultssupporting

confidence: 64%

Phosphatidylinositol-3 kinase activity controls survival and stemness of zebrafish hematopoietic stem/progenitor cells

Blokzijl-Franke

Ponsioen

Schulte‐Merker

et al. 2020

Preprint

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“…Unfortunately, not all biological questions can be translated into survival phenotypes, there being many other features that cannot be revealed by such an approach. To cope with this problem another type of cell sorting, named FACS, can be applied ( Baron et al, 2019 ; Voronin et al, 2020 ). It is based on fluorescence activation with the subpopulations being isolated based on their fluorescence signals.…”

Section: Large-scale Genome Screening By Crispr/dcas9mentioning

confidence: 99%

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems

Shakirova

Ovchinnikova

Дашинимаев

2020

Front. Bioeng. Biotechnol.

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The speed of reprogramming technologies evolution is rising dramatically in modern science. Both the scientific community and health workers depend on such developments due to the lack of safe autogenic cells and tissues for regenerative medicine, genome editing tools and reliable screening techniques. To perform experiments efficiently and to propel the fundamental science it is important to keep up with novel modifications and techniques that are being discovered almost weekly. One of them is CRISPR/Cas9 based genome and transcriptome editing. The aim of this article is to summarize currently existing CRISPR/Cas9 applications for cell reprogramming, mainly, to compare them with other non-CRISPR approaches and to highlight future perspectives and opportunities.

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“…It has been suggested that to estimate several important gene characteristics, the most favourable sequencing depth is around one read per cell per gene [ 153 ]. Alternatively, enrich the cell type of interest by using FACS, followed by scRNA-seq and use methods such as GateID to predict “nonintuitive” gating strategies based on scRNA-seq data [ 154 ] Will comparisons be made between different conditions (e.g., prime alone vs. prime-boost)? What are the qualities and expression levels of the marker genes of cell types of interest?…”

Section: A Experimental Considerations For Scrna-seq In Vaccinology mentioning

confidence: 99%

The Application of Single-Cell RNA Sequencing in Vaccinology

Noé

Cargill

Nielsen

et al. 2020

Journal of Immunology Research

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Single-cell RNA sequencing allows highly detailed profiling of cellular immune responses from limited-volume samples, advancing prospects of a new era of systems immunology. The power of single-cell RNA sequencing offers various opportunities to decipher the immune response to infectious diseases and vaccines. Here, we describe the potential uses of single-cell RNA sequencing methods in prophylactic vaccine development, concentrating on infectious diseases including COVID-19. Using examples from several diseases, we review how single-cell RNA sequencing has been used to evaluate the immunological response to different vaccine platforms and regimens. By highlighting published and unpublished single-cell RNA sequencing studies relevant to vaccinology, we discuss some general considerations how the field could be enriched with the widespread adoption of this technology.

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Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Cited by 53 publications

References 62 publications

Phosphatidylinositol-3 kinase activity controls survival and stemness of zebrafish hematopoietic stem/progenitor cells

Phosphatidylinositol-3 kinase activity controls survival and stemness of zebrafish hematopoietic stem/progenitor cells

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems

The Application of Single-Cell RNA Sequencing in Vaccinology

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