Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling: single cell RNA sequencing data

Meningeal single cell RNA sequencing data

Meningeal samples were collected from both dorsal and ventral skull, avoiding inclusion of choroid plexus. Samples were digested in 2.5 mg/mL Collagenase D (Cat. #11088858001; Roche) and 12.5 μL of 0.5 mg/mL DNAseI (Cat. #L5002139; Worthington), put on a shaker at 370C for 30 m, diluted with cold HBSS + 0.1% BSA, and mashed through a 70 μm cell strainer prior to sorting.

Data represent live, nucleated, singlet cells (DAPI-DRAQ5+) sorted on a BD FACS Aria Fusion into HBSS + 10% FBS prior to droplet encapsulation using 10x Genomics’ Drop-seq platform (Chromium v2).

10X chip lane is indicate by 'group' column

Group 1 = 4 pooled homecage control (unstressed) mice

Group 2 = 4 pooled homecage control (unstressed) mice

Group 3 = 4 pooled mice exposed to chronic social defeat for 14 days; tissue was collected 2 hours following final defeat

See the following repositories for data processing:

https://github.com/maryellenlynall/2019_bcell_stress/ (processing from raw files starts at bcellstress020.Rmd)

https://github.com/staceykigar/meningeal_neut/

We also provide a processed dataset (processed.RData) with assays 'counts' and 'logcounts' which is the processed single cell object saved at line "# Save object for upload to Zenodo" in script https://github.com/staceykigar/meningeal_neut/neutrophilstress01.Rmd 

Cluster annotations are in sce$Annotation

Neutrophil subcluster annotations are in sce$Subcluster

Sample condition is in sce$cond, where "HC" indicates homecage control and "SD" indicates chronic social defeat

10X chip lane is in sce$group