Code repository for locus coeruleus (LC) data analyses

This repository contains code scripts to reproduce analyses and figures in our manuscript:

• Weber and Divecha et al. (2023), The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife Reviewed Preprint.

Overview

We used a combination of spatially-resolved transcriptomics (10x Genomics Visium platform) and single-nucleus RNA-sequencing to characterize the molecular landscape of the LC region and the transcriptomic profile of LC neurons in the human brain.

The dataset is freely accessible in both interactive web-based and downloadable formats.

Our manuscript describes the data, analyses, and provides links to access the data.

Contents

Scripts to reproduce analyses and figures in manuscript:

• code/analyses/Visium/: scripts for analysis workflow for Visium data
• code/analyses/snRNAseq/: scripts for analysis workflow for snRNA-seq data

Preprocessing scripts:

• code/preprocessing/spaceranger/: scripts to run Space Ranger for pre-processing Visium data
• code/preprocessing/cellranger/: scripts to run Cell Ranger for pre-processing Visium data

Additional information

Path to project directory on our compute cluster: /dcs04/lieber/lcolladotor/pilotLC_LIBD001/locus-c/

Sample information: sample_info/

Web summaries from Space Ranger and Cell Ranger: web_summaries/