Abstract A decline in hematopoietic stem cell (HSC) function is believed to underlie hematological shortcomings with age; however, a comprehensive molecular understanding of these changes currently lacking. Here we provide evidence that transcriptional signature reported several previous studies on HSC aging linked stress-induced gene expression rather than aging. Our findings have strong implications for the design and interpretation studies.

Abstract As the scale of single-cell genomics experiments grows into millions, computational requirements to process this data are beyond reach many. Herein we present Scarf, a modularly designed Python package that seamlessly interoperates with other toolkits and allows for memory-efficient analysis millions cells on laptop or low-cost devices like single-board computers. We demonstrate Scarf’s memory compute-time efficiency by applying it largest existing RNA-Seq ATAC-Seq datasets. Scarf...

The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After 3 weeks culture, only 0.1% exhibited the input HSC phenotype, but these accounted almost all functional long-term activity. Input displayed varying potential vivo self-renewal, with alternative outcomes revealed by single-cell multimodal RNA ATAC sequencing profiling....

Knowledge of human fetal blood development and how it differs from adult is highly relevant to our understanding congenital immune disorders childhood leukemia, which the latter can originate in utero. Blood formation occurs waves that overlap time space, adding heterogeneity, necessitates single-cell approaches. Here, a combined immunophenotypic transcriptional map first trimester primitive presented. Using CITE-seq (cellular indexing transcriptomes epitopes by sequencing), molecular...

The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After 3 weeks culture, only 0.1% exhibited the input HSC phenotype, but these accounted almost all functional long-term activity. Input displayed varying potential vivo self-renewal, with alternative outcomes revealed by single-cell multimodal RNA ATAC sequencing profiling....

ABSTRACT Single-cell transcriptomics facilitates innovative approaches to define and identify cell types within tissues populations. An emerging interest in the cancer field is assess heterogeneity of transformed cells, including identification tumor-initiating cells based on similarities their normal counterparts. However, such mapping often confounded by large effects total gene expression programs introduced strong perturbations as an oncogenic event. Here, we present Nabo, a novel...

The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After three weeks culture, only 0.1% exhibited the input HSC phenotype, but these accounted almost all functional long-term activity. Input displayed varying potential vivo self-renewal, with alternative outcomes revealed by single cell multimodal RNA- ATAC-seq profiling....

The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After three weeks culture, only 0.1% exhibited the input HSC phenotype, but these accounted almost all functional long-term activity. Input displayed varying potential vivo self-renewal, with alternative outcomes revealed by single cell multimodal RNA- ATAC-seq profiling....

ABSTRACT The increasing capacity to perform large-scale single-cell genomic experiments continues outpace the computational requirements efficiently handle growing datasets. Herein we present Scarf, a modularly designed Python package that seamlessly interoperates with other toolkits and allows for memory-efficient analysis of millions cells on laptop or low-cost devices like single board computers. We demonstrate Scarf’s memory compute-time efficiency by applying it largest existing RNA-Seq...

ABSTRACT The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After three weeks culture, only 0.1% exhibited the input HSC phenotype, but these accounted almost all functional long-term activity. Input displayed varying potential vivo self-renewal, with alternative outcomes revealed by single cell multimodal RNA- ATAC-seq...

ABSTRACT Knowledge of human fetal blood development and how it differs from adult is highly relevant for our understanding congenital immune disorders as well childhood leukemia, the latter known to originate in utero. Blood production during occurs waves that overlap time space adding heterogeneity, which necessitates single cell approaches. Here, a combined immunophenotypic transcriptional map first trimester primitive presented. Using CITE-seq (Cellular Indexing Transcriptomes Epitopes by...