The single-cell transcriptional landscape of mammalian organogenesis

Nature, Год журнала: 2019, Номер 566(7745), С. 496 - 502

Опубликована: Фев. 20, 2019

Язык: Английский

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Current best practices in single‐cell RNA‐seq analysis: a tutorial

Molecular Systems Biology, Год журнала: 2019, Номер 15(6)

Опубликована: Июнь 1, 2019

Single-cell RNA-seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single-cell analysis methods. As more tools are becoming available, it increasingly difficult navigate landscape and produce up-to-date workflow analyse one's data. Here, we detail the steps typical analysis, including pre-processing (quality control, normalization, data correction, feature selection, dimensionality reduction) cell- gene-level downstream analysis. We formulate current best-practice recommendations these based on independent comparison studies. have integrated into workflow, which apply public dataset further illustrate how work in practice. Our documented case study can found https://www.github.com/theislab/single-cell-tutorial This review will serve as tutorial new entrants field, help established users update their pipelines.

Язык: Английский

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Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

Immunity, Год журнала: 2019, Номер 50(5), С. 1317 - 1334.e10

Опубликована: Апрель 9, 2019

Язык: Английский

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Eleven grand challenges in single-cell data science

Genome biology, Год журнала: 2020, Номер 21(1)

Опубликована: Фев. 7, 2020

Abstract The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell technology. Thousands—or even millions—of cells analyzed a single experiment amount to data revolution biology pose unique science problems. Here, we outline eleven challenges that will be central bringing this emerging field of forward. For each challenge, highlight motivating research questions, review prior work, formulate open This compendium is for established researchers, newcomers, students alike, highlighting interesting rewarding problems the coming years.

Язык: Английский

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Single-cell transcriptional diversity is a hallmark of developmental potential

Science, Год журнала: 2020, Номер 367(6476), С. 405 - 411

Опубликована: Янв. 24, 2020

More diversity at the top A detailed knowledge of cell differentiation hierarchies is important for understanding diverse biological processes such as organ development, tissue regeneration, and cancer. Single-cell RNA sequencing can help elucidate these hierarchies, but it requires reliable computational methods predicting lineage trajectories. Gulati et al. developed CytoTRACE, a framework based on simple observation that transcriptional diversity—the number genes expressed in cell—decreases during differentiation. CytoTRACE outperformed other several test cases was successfully applied to study cellular healthy tumor tissue. Science , this issue p. 405

Язык: Английский

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A single-cell molecular map of mouse gastrulation and early organogenesis

Nature, Год журнала: 2019, Номер 566(7745), С. 490 - 495

Опубликована: Фев. 1, 2019

Язык: Английский

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A human cell atlas of fetal gene expression

Science, Год журнала: 2020, Номер 370(6518)

Опубликована: Ноя. 12, 2020

The genomics of human development Understanding the trajectory a developing requires an understanding how genes are regulated and expressed. Two papers now present pooled approach using three levels combinatorial indexing to examine single-cell gene expression chromatin landscapes from 15 organs in fetal samples. Cao et al. focus on measurements RNA broadly distributed cell types provide insights into organ specificity. Domcke examined accessibility cells these identify regulatory elements that regulate expression. Together, analyses generate comprehensive atlases early development. Science , this issue p. eaba7721 eaba7612

Язык: Английский

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Lineage tracing meets single-cell omics: opportunities and challenges

Nature Reviews Genetics, Год журнала: 2020, Номер 21(7), С. 410 - 427

Опубликована: Март 31, 2020

Язык: Английский

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A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

Science, Год журнала: 2019, Номер 365(6459)

Опубликована: Сен. 5, 2019

Identifying terminal nematode cells Single-cell RNA sequencing provides the power to identify developmental trajectory of an organism. However, identifying temporal lineage cell development can be difficult without large-scale analyses. Packer et al. sequenced more than 80,000 from embryos roundworm Caenorhabditis elegans determine expression genes directing types. Because all somatic in a C. individual have been mapped, authors are able connect gene with lineages over time during development, noting stark transitions some cases. Science , this issue p. eaax1971

Язык: Английский

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Spatiotemporal structure of cell fate decisions in murine neural crest

Science, Год журнала: 2019, Номер 364(6444)

Опубликована: Июнь 6, 2019

Neural crest cells are embryonic progenitors that generate numerous cell types in vertebrates. With single-cell analysis, we show mouse trunk neural become biased toward neuronal lineages when they delaminate from the tube, whereas cranial acquire ectomesenchyme potential dependent on activation of transcription factor Twist1. The choices make to sensory, glial, autonomic, or mesenchymal can be formalized as a series sequential binary decisions. Each branch decision tree involves initial coactivation bipotential properties followed by gradual shifts commitment. Competing fate programs coactivated before fate-specific phenotypic traits. Determination specific is achieved increased synchronization relevant and concurrent repression competing programs.

Язык: Английский

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