Integrative single-cell analysis

T Stuart, R Satija - Nature reviews genetics, 2019 - nature.com
The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has
coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic …

From haematopoietic stem cells to complex differentiation landscapes

E Laurenti, B Göttgens - Nature, 2018 - nature.com
The development of mature blood cells from haematopoietic stem cells has long served as a
model for stem-cell research, with the haematopoietic differentiation tree being widely used …

Simultaneous epitope and transcriptome measurement in single cells

M Stoeckius, C Hafemeister, W Stephenson… - Nature …, 2017 - nature.com
High-throughput single-cell RNA sequencing has transformed our understanding of complex
cell populations, but it does not provide phenotypic information such as cell-surface protein …

BCG educates hematopoietic stem cells to generate protective innate immunity against tuberculosis

E Kaufmann, J Sanz, JL Dunn, N Khan, LE Mendonça… - Cell, 2018 - cell.com
The dogma that adaptive immunity is the only arm of the immune response with memory
capacity has been recently challenged by several studies demonstrating evidence for …

Guidelines for the use of flow cytometry and cell sorting in immunological studies

A Cossarizza, HD Chang, A Radbruch… - European journal of …, 2019 - Wiley Online Library
These guidelines are a consensus work of a considerable number of members of the
immunology and flow cytometry community. They provide the theory and key practical …

[HTML][HTML] A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

ATL Lun, DJ McCarthy, JC Marioni - F1000Research, 2016 - ncbi.nlm.nih.gov
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of
individual cells. This provides biological resolution that cannot be matched by bulk RNA …

Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis

AE Rodriguez-Fraticelli, C Weinreb, SW Wang… - Nature, 2020 - nature.com
Bone marrow transplantation therapy relies on the life-long regenerative capacity of
haematopoietic stem cells (HSCs),. HSCs present a complex variety of regenerative …

[HTML][HTML] An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells

S Bowling, D Sritharan, FG Osorio, M Nguyen… - Cell, 2020 - cell.com
Tracing the lineage history of cells is key to answering diverse and fundamental questions in
biology. Coupling of cell ancestry information with other molecular readouts represents an …

Single-cell transcriptomics to explore the immune system in health and disease

MJT Stubbington, O Rozenblatt-Rosen, A Regev… - Science, 2017 - science.org
The immune system varies in cell types, states, and locations. The complex networks,
interactions, and responses of immune cells produce diverse cellular ecosystems composed …

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

S Nestorowa, FK Hamey, B Pijuan Sala… - Blood, The Journal …, 2016 - ashpublications.org
Maintenance of the blood system requires balanced cell fate decisions by hematopoietic
stem and progenitor cells (HSPCs). Because cell fate choices are executed at the individual …