Computational workflow for investigating highly variable genes in single-cell RNA-seq across multiple time points and cell types

Arora, Jantarika Kumar; Opasawatchai, Anunya; Teichmann, Sarah A.; Matangkasombut, Ponpan; Charoensawan, Varodom

doi:10.1016/j.xpro.2023.102387

Cited by 4 publications

(2 citation statements)

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“…We followed an analysis procedure adapted from Arora et al, with details listed below (19). Bulk level hierarchical clustering: For each cluster in neutrophils, we generated a pseudobulk profile by calculating the average expression level for each gene using the RNA assay.…”

Section: Functional Annotation For Zebrafish Myeloid Subsetsmentioning

confidence: 99%

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Single-cell transcriptional landscape of temporal neutrophil response to burn wound in larval zebrafish

Hou,

Khatri,

Rindy

et al. 2024

Preprint

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Neutrophils accumulate early in tissue injury. However, the cellular and functional heterogeneity of neutrophils during homeostasis and in response to tissue damage remains unclear. Here, we use larval zebrafish to understand neutrophil responses to thermal injury. Single-cell transcriptional mapping of myeloid cells during a 3-day time course in burn and control larvae revealed distinct neutrophil subsets and their cell-cell interactions with macrophages across time and conditions. The trajectory formed by three zebrafish neutrophil subsets resembles human neutrophil maturation, with varying transition patterns between conditions. Through ligand-receptor cell-cell interaction analysis, we found neutrophils communicate more in burns in a pathway and temporal manner. Finally, we identified the correlation between zebrafish myeloid signatures and human burn severity, establishing GPR84+ neutrophils as a potential marker of early innate immune response in burns. This work builds the molecular foundation and a comparative single-cell genomic framework to identify neutrophil markers of tissue damage using model organisms.

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Section: Functional Annotation For Zebrafish Myeloid Subsetsmentioning

confidence: 99%

“…Bulk level PCA: Pseudobulk profiles were generated similarly as above. We added one step before performing PCA to bring the average expression matrix back to log scale, which was missing in the original pipeline (19). These profiles were used as input for PCA with scale.…”

Section: Functional Annotation For Zebrafish Myeloid Subsetsmentioning

confidence: 99%