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README.md

Single Cell Immune Profiling of Atherosclerotic Plaques

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This repository contains notebooks for interactively visualizing the single cell gene expression data from the study: Immune Profiling of Atherosclerotic Plaques Identifies Innate and Adaptive Dysregulations Associated with Ischemic Cerebrovascular Events (Fernandez et al.). The interactive visualizations are made using the single cell data analysis and visualization toolkit Clustergrammer2 and work best using the Chrome browser.

Launch Lab: https://mybinder.org/v2/gh/giannarelli-lab/Single-Cell-Immune-Profiling-of-Atherosclerotic-Plaques/master?urlpath=lab

citeseq_adt

Notebook Directory

CITE-seq Sample

Sample Cohort scRNA-seq

Ligand-Receptor Interaction Prediction

Click above notebook links to navigate to section and find NBViewer linkst to interactive notebooks.

1.0 CITE-seq PBMC and Plaque: ADT

Nbviewer

citeseq_adt_pbmc_plaque

Single cell antibody derived tag data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

1.1 CITE-seq PBMC and Plaque: GEX

Nbviewer

citeseq_gex_pbmc_plaque

Single cell gene expression data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

1.2 CITE-seq GEX Plaque: T Cells

Nbviewer

citeseq_gex_t_cells_plaque

Single cell gene expression data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

1.3 CITE-seq GEX Plaque: CD4 T Cells

Nbviewer

citeseq_gex_cd4_t_cells_plaque

Single cell gene expression data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

1.4 CITE-seq GEX Plaque: CD8 T Cells

Nbviewer

citeseq_gex_cd8_t_cells_plaque

Single cell gene expression data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

1.5 CITE-seq GEX Plaque: Macrophages

Nbviewer

citeseq_gex_macrophages_plaque

Single cell gene expression data data was obtained from plaque and PBMC from the same subject. Cell type was assigned based on ADT surface marker expression.

2.0 scRNA-seq Cohort: T Cells

Nbviewer

scrnaseq_cohort_t_cells

Single-cell gene expression data was obtained from atherosclerotic plaque samples from a cohort of six patients.

2.1 scRNA-seq Cohort: CD4 T Cells

Nbviewer

scrnaseq_cohort_cd4_t_cells

Single-cell gene expression data was obtained from atherosclerotic plaque samples from a cohort of six patients.

2.2 scRNA-seq Cohort: CD8 T Cells

Nbviewer

scrnaseq_cohort_cd8_t_cells

Single-cell gene expression data was obtained from atherosclerotic plaque samples from a cohort of six patients.

2.3 scRNA-seq Cohort: Macrophages

Nbviewer

scrnaseq_cohort_macrophages

Single-cell gene expression data was obtained from atherosclerotic plaque samples from a cohort of six patients.

3.0 Ligand-Receptor Sym-vs-Asym Differential Regulation

Nbviewer

lig-rec_sym-asym_diff_interactions

Putative ligand-receptor interactions between cell types were predicted based on the product of ligand and receptor expression across pairs of cell types. Differentially regulated interactions across symptomatic vs asymptomatic plaques are shown in interactive heatmaps.

Contact

https://www.mountsinai.org/profiles/chiara-giannarelli

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Immune Profiling of Atherosclerotic Plaques Identifies

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