NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE189031 Query DataSets for GSE189031
Status Public on Sep 01, 2022
Title Single cell RNA-sequencing of pleural cavity macrophages naïve and nematode-infected C57BL/6 and BALB/c mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The recent revolution in tissue-resident macrophage biology has resulted largely from murine studies performed in the C57BL/6 strain. Here, we provide a comprehensive analysis of immune cells in the pleural cavity using both C57BL/6 and BALB/c mice. Unlike C57BL/6 mice, naïve tissue-resident Large Cavity Macrophages (LCM) of BALB/c mice failed to fully implement the tissue residency programme. Following infection with a pleural-dwelling nematode these pre-existing differences were accentuated with LCM expansion occurring in C57BL/6 but not BALB/c mice. While infection drove monocyte recruitment in both strains, only in C57BL/6 mice were monocytes able to integrate into the resident pool. Monocyte to macrophage conversion required both T cells and IL-4Rα signalling. Host genetics are therefore a key influence on tissue resident macrophage biology, and during nematode infection Th2 cells control the differentiation pathway of tissue resident macrophages.
 
Overall design For the input of the single cell RNA sequencing, we chose the day 35 p.i. timepoint as this is when worm killing begins in C57BL/6 mice and monocyte influx begins in infected BALB/c mice. Pleural cavity immune cells were isolated from naïve and day 35 post infection L. sigmodontis-infected C57BL/6 and BALB/c mice. Cells were sorted by FACS to select Live single, lineage-CD45.2+Ter-119-CD11b+ cells, where lineage cocktail contained TCR-b, CD20, CD19, Ly6G, Nk1.1, CD90.2, CD5, IgM, CD3e and Siglec-F antibodies. Samples were loaded separately on 10X Genomics Chromium controller. 4 Separate cDNA libraries were created using the Single Cell 3’ Library Version 2 Kit. Library preparation was performed by University of Manchester Genomics technology core facility. The pooled Library was sequenced with paired-end reads using a full S2 lane of a NovaSeq-6000 (Illumina) by Edinburgh Genomics yielding 1750 million reads. Original fastq files are included. Sequencing reads in fastq format were aligned to the mm10 mouse transcriptome using Cell Ranger v3.0 (10 X Genomics) count function, quantifing Unique Molecular Identifiers (UMI) for each gene associated with each cell barcode. Samples were integrated and normalised using the Cell Ranger aggr function producing a gene versus cell expression matrix. Supplementary files contain analysed R/Python objects.
 
Contributor(s) Finlay CM, Parkinson J, Allen JE
Citation(s) 36948193
Submission date Nov 17, 2021
Last update date May 25, 2023
Contact name Conor M Finlay
E-mail(s) cofinlay@tcd.ie, conor.finlay@manchester.ac.uk
Organization name Trinity College Dublin
Department School of Medicine
Street address Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8
City Dublin
ZIP/Postal code D08 W9RT
Country Ireland
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM5693444 CF1 C57BL/6 Naïve
GSM5693445 CF2 BALB/c Naïve
GSM5693446 CF3 C57BL/6 Infected
Relations
BioProject PRJNA781228

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE189031_Merge_scv.h5ad.gz 1.8 Gb (ftp)(http) H5AD
GSE189031_RAW.tar 124.9 Mb (http)(custom) TAR (of TAR)
GSE189031_aggr_filtered_feature_bc_matrix.tar.gz 124.1 Mb (ftp)(http) TAR
GSE189031_sce.Rdata.gz 310.6 Mb (ftp)(http) RDATA
GSE189031_seurat.combined.Rdata.gz 2.7 Gb (ftp)(http) RDATA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap