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GEO help: Mouse over screen elements for information. |
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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
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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.
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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.
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Contributor(s) |
Finlay CM, Parkinson J, Allen JE |
Citation(s) |
36948193 |
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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
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Organization name |
Trinity College Dublin
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Department |
School of Medicine
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Street address |
Trinity Translational Medicine Institute, Trinity College Dublin, St. James' Hospital Campus, Trinity College Dublin, Dublin 8
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City |
Dublin |
ZIP/Postal code |
D08 W9RT |
Country |
Ireland |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (4)
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Relations |
BioProject |
PRJNA781228 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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