Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell RNA sequencing of murine lungs of SPAM deleter mice after alveolar macrophage depletion

ABSTRACT: Single cell sequencing dataset of CD45+ and CD45- lung cells in a timecourse after intratracheal diphtheria toxin treatment in the SPAM-deleter model. Sequencing data was obtained at following timepoints: 0h, 12h, 24h, 2 days, 5 days, 8 days and 14 days.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus musculus

SUBMITTER: Stijn Verwaerde

PROVIDER: E-MTAB-16590 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Single-cell RNA sequencing of murine lung in steady state, after IL-33 treatment or HDM treatment

Project description:Single cell RNA sequencing of the lung in steady state, after 1 or 3 doses of IL-33 or after HDM treatment Exp1: steady state lung cells (both CD45- as CD45+) from 4 untreated mice. Cells from distinct replicates are labeled with unique HTO barcodes. Exp2: lung cells (both CD45- as CD45+) from 2 mice (PBS intratracheal treatment), 4 mice (1xIL33 intratracheal treatment) and 4 mice (3 x IL33 intratracheal treatment). Cells from distinct replicates are labeled with unique HTO barcodes. Exp3: lung, bone marrow and blood cells (CD45+ CD3- CD19-) from 3 mice (House dust mite intratracheal (HDM) treatment and 14 days later PBS intranasal treatment on 4 consecutive days) and 3 mice (HDM treatment and 14 days later HDM intranasal treatment on 4 consecutive days). Mice were pooled and different organs were labeled with unique HTO barcodes. In all cases, collection of the samples was performed 24 hours after the last treatment. More experimental details can be found in the STAR methods section of the publication.

2025-12-12 | E-MTAB-16099 | biostudies-arrayexpress

Effect of the combined neonatal pneumonia virus of mice infection and house dust mite exposure on the trancriptional profile of dendritic cells in the lung

Project description:scRNAseq experiment of mouse dendritic cells in the lung after intranasal infection with pneumonia virus of mice (7 days postnatally) or mock and/or intranasal house dust mite or PBS sensitisation (14 days postnatally). Cells were isolated when mice were 15 days old. No prior bronchoalveolar lavage was taken and mice received intravenous labeling of immune cells with CD45 to distuinguish between circulating and lung resident immune cells.

2025-10-22 | E-MTAB-15850 | biostudies-arrayexpress

scRNA-seq of CD45+ cells from mouse B16F10 melanoma treated with anti-PD-1 antibody against untreated control

Project description:The B16F10 mouse melanoma cells were inoculated onto the right flank of C57BL/6J mice and every 4 days, anti-PD-1 antibody was injected through the tail vein. In total, 3 doses of immunotherapy treatments were given to the experimental animals. Two days after the last treatment, all tumors including treated and untreated control were collected, cut and digested. The resulted tumor sample single cell suspensions were next red blood cell lysed, stained and then proceeded for FACS sorting to get the live CD45+ intratumoral immune cells. The CD45+ cells from the tumor samples were subsequently count to adjust cell concentration and then used as input for scRNA-seq library construction using the 10x Genomics GEM-X Universal 3' Gene Expression v4 kit following the manufacturer’s protocol.

2026-05-16 | E-MTAB-16990 | biostudies-arrayexpress

scRNA-seq analysis of lung CD64-expressing mononuclear cells, patrolling and classical monocytes from steady-state C57BL/6J mice

Project description:We sought to evaluate in an unbiased way the heterogeneity of lung interstitial macrophages and their relationship with alveolar macrophages, lung Ly-6Chi classical monocytes and Ly-6Clo patrolling monocytes, by single cell RNA-Seq.

2019-07-31 | E-MTAB-7678 | biostudies-arrayexpress

Single cell RNA sequencing analysis of mouse resident and infiltrating immune cells during acute kidney injury and fibrosis

Project description:To obtain an unbiased characterization of the resident and infiltrating immune cell populations of mouse kidneys in healthy and diseased states, we performed single cell RNA-seq of facs-sorted CD45+ immune cells and CD4+ T cells from naïve and injured kidneys, at selected time points.

2020-01-31 | E-MTAB-8002 | biostudies-arrayexpress

Single cell RNA sequencing of myeloid cells from the aortas of ApoE-/- mice fed a high fat diet for 12-16 weeks

Project description:scRNA-seq of CD45+CD11b+ or CD45+CD11b+ CD64low-high cells from the whole aortas of ApoE-/- mice fed a high fat diet (HFD) for 12-16 weeks using the Chromium 10X genomics platform (9 mice were pooled each experiment; three independent experiments).

2021-10-28 | E-MTAB-10743 | biostudies-arrayexpress

Single-cell RNA-Seq of entire ventricles of C57BL/6J and B6.Rag2del mice after myocardial infarction

Project description:We compared the cellular and molecular outcome following permanent LAD ligation in wildtype and T- and B cell deficient Rag2del mice. Our results demonstrate that the significant changes in the cardiac immune response following myocardial infarction (MI). 8-12 weeks old, male and female C57BL/6J mice (Charles River, Wilmington, MA, USA) and B6.Rag2del mice (Jackson laboratory, Bar Harbor, ME, USA) were used for this study. Seven days after MI, entire mouse ventricles were isolated and enzymatically digested. Cells were then labelled with CD45 magnetic beads (Miltenyi Biotec, Germany) and positively enriched using the AutoMACS instrument (Miltenyi Biotec, Germany). Viable macrophages/monocytes (CD45+CD11b+CD11c-DAPI-Lactadherinlo), dendritic cells (CD45+CD11b+CD11c+ DAPI-Lactadherinlo), and NK cells (CD45+CD11b-CD11c+NK1.1+ DAPI-Lactadherinlo) were then sorted on the BD FACSAriaTM IIIu (Becton Dickinson, Franklin Lakes, NJ, USA) roughly in a 1:1:1 ratio into DMEM containing 10% FCS before processing for 10× Genomics single-cell RNA sequencing (scRNA-Seq). Libraries for scRNA-Seq were constructed according to the 10× Genomics protocol using the GemCode Single-Cell 3′ Gel Bead and Library V3 Kit. Quality of amplified cDNA and final libraries were evaluated on the 2100 Bioanalyzer instrument (Agilent) using a High Sensitivity NGS Analysis Kit (Advanced Analytical). Subsequent sequencing was conducted on the HighSeq4000 Sequencing System using the HiSeq SBS and HiSeq PE Cluster Kit V4 (all Illumina, San Die-go, CA. USA).

2023-07-20 | E-MTAB-13147 | biostudies-arrayexpress

Single cell RNA sequencing of myeloid cells from the aortas of ApoE-/- and ApoE-/- Clec4a2-/- mice fed a high fat diet for 12 weeks

Project description:CD45+CD11b+ cells from the whole aortas of ApoE-/- and ApoE-/- Clec4a2-/- mice fed a high fat diet (HFD) for 12 weeks using using 10X genomics platform (9 mice in each genotype were pooled; one experiment).

2021-10-28 | E-MTAB-10746 | biostudies-arrayexpress

Transcriptional remodeling of human dermal blood vascular and lymphatic endothelial cells in psoriasis

Project description:Single-cell transcriptomic profiling of CD45-CD31+ endothelial cells derived from healthy and psoriatic human skin using the 10x Genomics platform.

2022-05-26 | E-MTAB-11218 | biostudies-arrayexpress

A single cell RNA-seq analysis of cardiac fibroblasts from pressure-overloaded mouse hearts

Project description:To verify the hypothesis that there are distinct subsets of cardiac fibroblasts, we performed single-cell RNA sequencing analysis of cardiac fibroblasts from pressure-overloaded ventricles.

2021-09-22 | E-MTAB-9839 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data