A Single Cell Transcriptomics Map of Paracrine Networks in the Intrinsic Cardiac Nervous System

We developed a spatially-tracked single neuron transcriptomics map of an intrinsic cardiac ganglion, the right atrial ganglionic plexus (RAGP) that is a critical mediator of sinoatrial node (SAN) activity. This 3D representation of RAGP used neuronal tracing to extensively map the spatial distribution of the subset of neurons that project to the SAN. RNA-seq of laser capture microdissected neurons revealed a distinct composition of RAGP neurons compared to the central nervous system and a surprising finding that cholinergic and catecholaminergic markers are coexpressed, suggesting multipotential phenotypes that can drive neuroplasticity within RAGP. High-throughput qPCR of hundreds of laser capture microdissected single neurons confirmed these findings and revealed a high dimensionality of neuromodulatory factors that contribute to dynamic control of the heart. Neuropeptide-receptor coexpression analysis revealed a combinatorial paracrine neuromodulatory network within RAGP informing follow-on studies on the vagal control of RAGP to regulate cardiac function in health and disease

A single cell transcriptomics map of paracrine networks in the intrinsic cardiac nervous system.

We developed a spatially-tracked single neuron transcriptomics map of an intrinsic cardiac ganglion, the right atrial ganglionic plexus (RAGP) that is a critical mediator of sinoatrial node (SAN) activity. This 3D representation of RAGP used neuronal tracing to extensively map the spatial distribution of the subset of neurons that project to the SAN. RNA-seq of laser capture microdissected neurons revealed a distinct composition of RAGP neurons compared to the central nervous system and a surprising finding that cholinergic and catecholaminergic markers are coexpressed, suggesting multipotential phenotypes that can drive neuroplasticity within RAGP. High-throughput qPCR of hundreds of laser capture microdissected single neurons confirmed these findings and revealed a high dimensionality of neuromodulatory factors that contribute to dynamic control of the heart. Neuropeptide-receptor coexpression analysis revealed a combinatorial paracrine neuromodulatory network within RAGP informing follow-on studies on the vagal control of RAGP to regulate cardiac function in health and disease

A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs.

This protocol explains how to use the online integrated pipeline 'peak-motifs' (http://rsat.ulb.ac.be/rsat/) to predict motifs and binding sites in full-size peak sets obtained by chromatin immunoprecipitation-sequencing (ChIP-seq) or related technologies. The workflow combines four time- and memory-efficient motif discovery algorithms to extract significant motifs from the sequences. Discovered motifs are compared with databases of known motifs to identify potentially bound transcription factors. Sequences are scanned to predict transcription factor binding sites and analyze their enrichment and positional distribution relative to peak centers. Peaks and binding sites are exported as BED tracks that can be uploaded into the University of California Santa Cruz (UCSC) genome browser for visualization in the genomic context. This protocol is illustrated with the analysis of a set of 6,000 peaks (8 Mb in total) bound by the Drosophila transcription factor Krüppel. The complete workflow is achieved in about 25 min of computational time on the Regulatory Sequence Analysis Tools (RSAT) Web server. This protocol can be followed in about 1 h.Journal ArticleResearch Support, Non-U.S. Gov'tSCOPUS: ar.jinfo:eu-repo/semantics/publishe

Additional file 3: of Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics

R Code used to analyze the single cell data used in this study. (R 20 kb