A single-cell transcriptome atlas for zebrafish development

Farnsworth, Dylan; Saunders, Lauren; Miller, Adam C.

doi:10.1016/j.ydbio.2019.11.008

Cited by 241 publications

(319 citation statements)

References 59 publications

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“…To determine if this was the case, we used a publicly available 3' scRNA-seq dataset obtained from zebrafish embryos at 5 dpf using the 10x Genomics platform (Farnsworth et al, 2019). In this case, we separately quantified mapped reads from this dataset to Ens95 and V4.2 annotations using the CellRanger pipeline followed by filtering, clustering, and differential expression analysis using Seurat (Stuart et al, 2019).…”

Section: V42 Improves Analysis Of Single-cell Rna-seq Data In Zebrafishmentioning

confidence: 99%

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An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Lawson

Shin

et al. 2020

eLife

116

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The zebrafish is ideal for studying embryogenesis and is increasingly applied to model human disease. In these contexts, RNA-sequencing (RNA-seq) provides mechanistic insights by identifying transcriptome changes between experimental conditions. Application of RNA-seq relies on accurate transcript annotation for a genome of interest. Here, we find discrepancies in analysis from RNA-seq datasets quantified using Ensembl and RefSeq zebrafish annotations. These issues were due, in part, to variably annotated 3' untranslated regions and thousands of gene models missing from each annotation. Since these discrepancies could compromise downstream analyses and biological reproducibility, we built a more comprehensive zebrafish transcriptome annotation that addresses these deficiencies. Our annotation improves detection of cell type-specific genes in both bulk and single cell RNA-seq datasets, where it also improves resolution of cell clustering. Thus, we demonstrate that our new transcriptome annotation can outperform existing annotations, providing an important resource for zebrafish researchers.

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Section: V42 Improves Analysis Of Single-cell Rna-seq Data In Zebrafishmentioning

confidence: 99%

“…Single-cell RNA-seq analysis. We downloaded scRNA-seq reads from whole zebrafish embryos at 5 dpf from the Sequence Read Archive (SRR10095965, Farnsworth et al, 2019).…”

Section: Annotation Of Novel Locimentioning

confidence: 99%

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Lawson

Shin

et al. 2020

eLife

116

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“…It has become a powerful tool to identify cell subpopulations sharing similar transcriptome within a population, as well as to provide information related to cell fate, development, lineage, physiology, homeostasis and underlying molecular mechanisms (2,5,6). The use of this recent technique has been described in humans (7)(8)(9), mice (10) and other species (11,12) in various conditions and samples. In dogs, the use of this technique has not yet been reported so far.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the Bronchoalveolar Lavage Fluid by Single Cell Gene Expression Analysis in Healthy Dogs: A Promising Technique

et al. 2020

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Single-cell mRNA-sequencing (scRNA-seq) is a technique which enables unbiased, high throughput and high-resolution transcriptomic analysis of the heterogeneity of cells within a population. This recent technique has been described in humans, mice and other species in various conditions to cluster cells in populations and identify new subpopulations, as well as to study the gene expression of cells in various tissues, conditions and origins. In dogs, a species for which markers of cell populations are often limiting, scRNA-seq presents with elevated yet untested potential for the study of tissue composition. As a proof of principle, we used scRNA-seq to identify cellular populations of the bronchoalveolar lavage fluid (BALF) in healthy dogs (n = 4). A total of 5,710 cells were obtained and analyzed by scRNA-seq. Fourteen distinct clusters of cells were identified, further identified as macrophages/monocytes (4 clusters), T cells (2 clusters) and B cells (1 cluster), neutrophils (1 cluster), mast cells (1 cluster), mature or immature dendritic cells (1 cluster each), ciliated or non-ciliated epithelial cells (1 cluster each) and cycling cells (1 cluster). We used for the first time in dogs the scRNA-seq to investigate cellular subpopulations of the BALF of dog. This study hence expands our knowledge on dog lung immune cell populations, paves the way for the investigation at single-cell level of lower respiratory diseases in dogs, and establishes that scRNA-seq is a powerful tool for the study of dog tissue composition.

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“…Cell cluster biomarkers were examined using the Seurat FindMarkers function. To annotate and label cells from the 32 identi ed clusters, we compared our single cell sequencing data to the zebra sh single cell atlas 14 . Seurat FindTransferAnchors and TransferData functions were used to integrate our single cell sequencing data set with the zebra sh single cell atlas and transfer cell annotation labels.…”

Section: Transient Injections and Heat Shockmentioning

confidence: 99%

Induced in vivo transdifferentiation of vertebrate muscle into early endoderm-like cells

Dong¹,

Lancman²,

Campbell³

et al. 2020

Preprint

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The extent to which differentiated cells, while remaining in their native microenvironment, can be reprogrammed to assume a different identity will reveal fundamental insight into cellular plasticity and impact regenerative medicine. To investigate in vivo cell lineage potential, we leveraged the zebrafish as a practical vertebrate platform to determine factors and mechanisms necessary to induce differentiated cells of one germ layer to adopt the lineage of another. We discovered that ectopic co-expression of Sox32 and Oct4 in several non-endoderm lineages, including skeletal muscle, can specifically trigger an early endoderm genetic program in a cell-autonomous manner. Gene expression, live imaging, and functional studies reveal that the endoderm-induced muscle cells lose muscle gene expression and morphology, while specifically gaining endoderm organogenesis lineage markers, such as the pancreatic specification genes, hhex and ptf1a, via a mechanism resembling normal development. Endoderm induction by a pluripotent defective form of Oct4, endoderm markers appearing prior to loss of muscle cell morphology, and a lack of mesoderm, ectoderm, dedifferentiation, and pluripotency gene activation, together, suggests that reprogramming is endoderm specific and occurs via direct transdifferentiation. Our work demonstrates that within a living vertebrate animal, differentiated cells can be induced to directly adopt the identity of a completely unrelated cell lineage, while remaining in a distinct microenvironment, suggesting that differentiated cells in vivo may be more amenable to lineage conversion than previously appreciated. This discovery of extensive lineage potential of differentiated cells, in vivo, challenges our understanding of cell lineage restriction and may pave the way towards new in vivo sources of replacement cells for degenerative diseases such as diabetes.

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A single-cell transcriptome atlas for zebrafish development

Cited by 241 publications

References 59 publications

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

An improved zebrafish transcriptome annotation for sensitive and comprehensive detection of cell type-specific genes

Characterization of the Bronchoalveolar Lavage Fluid by Single Cell Gene Expression Analysis in Healthy Dogs: A Promising Technique

Induced in vivo transdifferentiation of vertebrate muscle into early endoderm-like cells

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