GEO series

CITE-Seq analysis of FACS-sorted live human CD45+ cells isolated from the ears of huNOG-EXL mice in a model of atopic dermatitis

GSE220685 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2025/02/08 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Mus musculus (mouse)
Samples: 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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: Ucenprubart is an agonistic antibody to CD200R with the potential to treat inflammatory skin disease: preclinical development and a phase 1 clinical studyNature communications · 2025

Summary (written by the submitters)

CD200R is an immune checkpoint receptor of the IgG family that is primarily expressed on cells of the myeloid lineage. In vivo studies with knockout mice of either the receptor or its ligand, CD200, have demonstrated that it is an inhibitory receptor capable of negatively regulating immune responses. Previous work using agonistic antibodies to mouse CD200R showed inhibition of mast cell activation in multiple preclinical models of autoimmune diseases.

Read the full summary ↓

We developed an agonistic antibody to the human CD200 receptor to downregulate the immune system human inflammatory conditions. Ucenprubart, is a humanized IgG4 monoclonal antibody that binds and agonizes human CD200R to suppress cellular activity in CD200R-expressing cells.The antibody was engineered to have desired properties for agonism and cross-reactivity to cyno CD200R. In vivo the antibody demonstrated efficacy in a humanized mouse model of contact hypersensitivity as well as passive cutaneous anaphylaxis in cynomolgus monkeys.

Published in

Ucenprubart is an agonistic antibody to CD200R with the potential to treat inflammatory skin disease: preclinical development and a phase 1 clinical study

Koester A, Witcher DR, Lee M et al. · Nature communications 2025 · PMID 40312358 · doi:10.1038/s41467-025-59147-w

This dataset

Open GSE220685 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 GSE220685_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 PRJNA911154 and SRA study SRP412500. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40312358) ↗

Study design

12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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

GSM6809578 CD200R_Ear, Replicate 1, mRNA-derived cDNA
GSM6809579 CD200R_Ear, Replicate 2, mRNA-derived cDNA
GSM6809580 Dupilumab_Ear, Replicate 1, mRNA-derived cDNA
GSM6809581 Dupilumab_Ear, Replicate2, mRNA-derived cDNA
GSM6809582 Isotype_Ear, Replicate1, mRNA-derived cDNA
GSM6809583 Isotype_Ear, Replicate2, mRNA-derived cDNA
GSM6809584 CD200R_Ear, Replicate 1, ADT-derived cDNA
GSM6809585 CD200R_Ear, Replicate 2, ADT-derived cDNA
GSM6809586 Dupilumab_Ear, Replicate 1, ADT-derived cDNA
GSM6809587 Dupilumab_Ear, Replicate2, ADT-derived cDNA
GSM6809588 Isotype_Ear, Replicate1, ADT-derived cDNA
GSM6809589 Isotype_Ear, Replicate2, ADT-derived cDNA

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GSE317004 CITE-seq of cardiac CD45+ leukocytes in mice with myocardial infarction and NK cell depletion 3 samples shares cd45, cite-seq
GSE297921 Single-cell sequencing of CD45+ cells isolated from nasal mucosa of mice 18 samples shares cd45, isolated
GSE279330 Tumor CD45+ cells and spleen LY6G+ PMNs isolated from Hdc-GFP mice with subcutaneous ACKP syngeneic GC line-established tumors and treated with TFF2-MSA and/or anti-PD-1 therapies. 8 samples shares cd45, isolated
GSE260482 Gene expression profile at single cell level of CD45+ immune cells from 4TO7 cells (Ctrl or Tim3-KD) liver metastasis at different timepoints 6 samples shares cd45, live
GSE261246 Gene expression profile at the single cell level of CD45+ CD11b+ cells isolated from the brain and bone marrow of mice either untreated or conditioned and transplanted with mouse hematopoietic stem and progenitor cells (HSPCs) expanded in culture. 4 samples shares cd45, isolated
GSE241877 Gene expression profile at the single cell level of CD45+ CD11b+ cells isolated from the brain and bone marrow of mice either untreated or conditioned and transplanted with total bone marrow. 4 samples shares cd45, isolated
GSE271786 Single Cell Gene Expression Profiling of CD45+ Cells in Mouse Liver with or without Empagliflozin (EMPA) Treatment 4 samples shares cd45, live

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