GEO series

CCR1 and CCR2 co-expression on monocytes is nonredundant and delineates a distinct monocyte subpopulation. [RNA-Seq]

GSE251646 Mus musculus (mouse) Single-cell RNA-seq 19 samples Submitted 2024/07/10 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 19 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 19 samples: 5 conditions, mostly with about 4 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: CCR1 and CCR2 Coexpression on Monocytes Is Nonredundant and Delineates a Distinct Monocyte SubpopulationJournal of immunology (Baltimore, Md. : 1950) · 2024

Summary (written by the submitters)

The interactions between chemokines and their receptors, particularly in the context of inflammation, are complex with individual receptors binding multiple ligands and individual ligands interacting with multiple receptors. In addition, there are numerous reports of simultaneous co-expression of multiple inflammatory chemokine receptors on individual inflammatory leukocyte subtypes.

Read the full summary ↓

Overall, this has previously been interpreted as redundancy and proposed as a protective mechanism to ensure that the inflammatory response is robust. In contrast we have hypothesised that the system is not redundant but exquisitely subtle. Our interests relate to the receptors CCR1, CCR2, CCR3 and CCR5 which, together, regulate non-neutrophilic myeloid cell recruitment to inflammatory sites. Here we demonstrate that, whilst most murine monocytes exclusively express CCR2, there is a small subpopulation, which is expanded during inflammation, which co-expresses CCR1 and CCR2. Combinations of transcript and functional analysis demonstrate that this is not redundant expression and that co-expression of CCR1 and CCR2 marks a phenotypically distinct population of monocytes characterised by expression of genes otherwise typically associated with neutrophils. Single cell RNA sequencing confirms this as a monodisperse population of atypical monocytes. This monocytic population has been previously described as having immunosuppressive activity. Overall, our data confirm combinatorial chemokine receptor expression by a subpopulation of monocytes but demonstrate that this is not redundant expression and marks a discrete monocytic population.

Published in

CCR1 and CCR2 Coexpression on Monocytes Is Nonredundant and Delineates a Distinct Monocyte Subpopulation

Medina-Ruiz L, Bartolini R, Mathie H et al. · Journal of immunology (Baltimore, Md. : 1950) 2024 · PMID 38829123 · doi:10.4049/jimmunol.2400007

This dataset

Open GSE251646 in finder → Find more mouse RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE251646_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1055013 and SRA study SRP479139. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38829123) ↗

Study design

5 conditions, mostly with about 4 replicates each

resting_CCR1_2 ×4 resting_CCR2 ×4 inflamed_CCR1 ×4 inflamed_CCR2 ×4 inflamed_CCR1_2 ×3

Supports a between-group comparison across 19 samples.

How we read this: 5 replicated groups read from 19 sample titles; they account for 19 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM7984559 resting_CCR1_2_rep1 resting_CCR1_2
GSM7984560 resting_CCR1_2_rep2 resting_CCR1_2
GSM7984561 resting_CCR1_2_rep3 resting_CCR1_2
GSM7984562 resting_CCR1_2_rep4 resting_CCR1_2
GSM7984563 resting_CCR2_rep1 resting_CCR2
GSM7984564 resting_CCR2_rep2 resting_CCR2
GSM7984565 resting_CCR2_rep3 resting_CCR2
GSM7984566 resting_CCR2_rep4 resting_CCR2
GSM7984567 inflamed_CCR1_2_rep2 inflamed_CCR1_2
GSM7984568 inflamed_CCR1_2_rep3 inflamed_CCR1_2
GSM7984569 inflamed_CCR1_2_rep4 inflamed_CCR1_2
GSM7984570 inflamed_CCR1_rep1 inflamed_CCR1
GSM7984571 inflamed_CCR1_rep2 inflamed_CCR1
GSM7984572 inflamed_CCR1_rep3 inflamed_CCR1
GSM7984573 inflamed_CCR1_rep4 inflamed_CCR1
GSM7984574 inflamed_CCR2_rep1 inflamed_CCR2
GSM7984575 inflamed_CCR2_rep2 inflamed_CCR2
GSM7984576 inflamed_CCR2_rep3 inflamed_CCR2
GSM7984577 inflamed_CCR2_rep4 inflamed_CCR2

Datasets on a similar topic

GSE251648 CCR1 and CCR2 co-expression on monocytes is nonredundant and delineates a distinct monocyte subpopulation. 20 samples shares ccr1, ccr2, co-expression, subpopulation, nonredundant, delineates, monocytes, distinct
GSE251647 CCR1 and CCR2 co-expression on monocytes is non-redundant and delineates a distinct monocyte subpopulation. [scRNA-Seq] 1 samples shares ccr1, ccr2, co-expression, subpopulation, delineates, monocytes, distinct
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GSE268156 CCR2+ monocytes promote white matter injury and cognitive dysfunction after myocardial infarction 2 samples shares ccr2, monocytes
GSE205991 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [deep single-cell RNA-seq] 2148 samples shares subpopulation, distinct

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