Christopher S. McGinnis
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View article: Cell cycle-coupled transcriptional network orchestrates human B cell fate bifurcation
Cell cycle-coupled transcriptional network orchestrates human B cell fate bifurcation Open
SUMMARY Antibody responses are determined by activated B cells bifurcating into plasmablasts (PBs) and germinal center B cells (GCBCs). Gene regulatory networks (GRNs) underlying human B cell fate choice remain uncharted. Temporally resolv…
View article: Translation dysregulation in cancer as a source for targetable antigens
Translation dysregulation in cancer as a source for targetable antigens Open
Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may r…
View article: Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC
Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC Open
Large-scale scATAC-seq experiments are challenging because of their costs, lengthy protocols, and confounding batch effects. Several sample multiplexing technologies aim to address these challenges, but do not remove batch effects introduc…
View article: Mapping enhancer-gene regulatory interactions from single-cell data
Mapping enhancer-gene regulatory interactions from single-cell data Open
Mapping enhancers and their target genes in specific cell types is crucial for understanding gene regulation and human disease genetics. However, accurately predicting enhancer-gene regulatory interactions from single-cell datasets has bee…
View article: Single-cell analysis of breast cancer metastasis reveals epithelial-mesenchymal plasticity signatures associated with poor outcomes
Single-cell analysis of breast cancer metastasis reveals epithelial-mesenchymal plasticity signatures associated with poor outcomes Open
Metastasis is the leading cause of cancer-related deaths. It is unclear how intratumor heterogeneity (ITH) contributes to metastasis and how metastatic cells adapt to distant tissue environments. The study of these adaptations is challenge…
View article: MULTI-seq sample multiplexing for 10x Genomics RNA+ATAC multiomic profiling v1
MULTI-seq sample multiplexing for 10x Genomics RNA+ATAC multiomic profiling v1 Open
This protocol describes the application of the MULTI-seq sample multiplexing technology (McGinnis, Patterson, et al., 2019, Nature Methods) for single-cell RNA+ATAC multiomic profiling using the 10x Genomics platform. This protocol is demo…
View article: Patterning and folding of intestinal villi by active mesenchymal dewetting
Patterning and folding of intestinal villi by active mesenchymal dewetting Open
Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molec…
View article: Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains
Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains Open
A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to c…
View article: Patterning and folding of intestinal villi by active mesenchymal dewetting
Patterning and folding of intestinal villi by active mesenchymal dewetting Open
Tissue folding generates structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, the numerous finger-like protrusions that are essential for nutrien…
View article: Single-cell RNA sequencing of 76,535 capillary PBMCs from 3 donors across 28 samples, freshly isolated or on ice for 24h with manual 4-layer annotation hierarchy
Single-cell RNA sequencing of 76,535 capillary PBMCs from 3 donors across 28 samples, freshly isolated or on ice for 24h with manual 4-layer annotation hierarchy Open
Sample Procurement Samples were collected directly from participants as part of ImYoo's "Single-cell immune profiling from self-collected capillary blood" study, approved by Advarra IRB (Protocol #Pro00057361). Sample Processing Whole capi…
View article: Single-cell RNA sequencing of 76,535 capillary PBMCs from 3 donors across 28 samples, freshly isolated or on ice for 24h with manual 4-layer annotation hierarchy
Single-cell RNA sequencing of 76,535 capillary PBMCs from 3 donors across 28 samples, freshly isolated or on ice for 24h with manual 4-layer annotation hierarchy Open
Sample Procurement Samples were collected directly from participants as part of ImYoo's "Single-cell immune profiling from self-collected capillary blood" study, approved by Advarra IRB (Protocol #Pro00057361). Sample Processing Whole capi…
View article: The temporal progression of immune remodeling during metastasis
The temporal progression of immune remodeling during metastasis Open
SUMMARY Tumor metastasis requires systemic remodeling of distant organ microenvironments which impacts immune cell phenotypes, population structure, and intercellular communication networks. However, our understanding of immune phenotypic …
View article: D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response
D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response Open
Gene regulatory networks within cells modulate the expression of the genome in response to signals and changing environmental conditions. Reconstructions of gene regulatory networks can reveal the information processing and control princip…
View article: Therapeutic algebra of immunomodulatory drug responses at single-cell resolution
Therapeutic algebra of immunomodulatory drug responses at single-cell resolution Open
Therapeutic modulation of immune states is central to the treatment of human disease. However, how drugs and drug combinations impact the diverse cell types in the human immune system remains poorly understood at the transcriptome scale. H…
View article: Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution
Dissecting the contributions of tumor heterogeneity on metastasis at single-cell resolution Open
Metastasis is the leading cause of cancer-related deaths, but metastasis research is challenged by limited access to patient material and a lack of experimental models that appropriately recapitulate tumor heterogeneity. Here, we analyzed …
View article: Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution
Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution Open
The rise and fall of estrogen and progesterone across menstrual cycles and during pregnancy regulates breast development and modifies cancer risk. How these hormones impact each cell type in the breast remains poorly understood because the…
View article: Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia
Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia Open
Significance During brain development, neurons are generated by spatially and temporally distinct processes that remain to be fully characterized. The ganglionic eminences (GEs) in the embryonic subpallium give rise to GABAergic and cholin…
View article: Interactive VISION reports for "KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
Interactive VISION reports for "KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution" Open
This repository contains VISION reports for the KP-Tracer tumors described in the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al bioRxiv 2021). In this study, single…
View article: Interactive VISION reports for "KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
Interactive VISION reports for "KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution" Open
This repository contains VISION reports for the KP-Tracer tumors described in the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al bioRxiv 2021). In this study, single…
View article: Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution" Open
This repository contains processed data associated with the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al bioRxiv 2021). In this study, single-cell lineage tracing …
View article: Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution"
Processed data for KP-Tracer Tumors from study "Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution" Open
This repository contains processed data associated with the manuscript "Lineage Recording Reveals the Phylodynamics, Plasticity, and Paths of Tumor Evolution" (Yang*, Jones*, et al bioRxiv 2021). In this study, single-cell lineage tracing …
View article: Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution
Lineage Recording Reveals the Phylodynamics, Plasticity and Paths of Tumor Evolution Open
SUMMARY Tumor evolution is driven by the progressive acquisition of genetic and epigenetic alterations that enable uncontrolled growth, expansion to neighboring and distal tissues, and therapeutic resistance. The study of phylogenetic rela…