GEO series

A neuro-mesenchymal cell subpopulation characterises the subaortic hematopoietic stem cell niche

GSE239434 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2024/03/11 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2 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: 2 samples
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: A multistep computational approach reveals a neuro-mesenchymal cell population in the embryonic hematopoietic stem cell nicheDevelopment (Cambridge, England) · 2024

Summary (written by the submitters)

The first hematopoietic stem and progenitor cells (HSPCs) emerge in the embryonic dorsal aorta of midgestation mouse embryo, but the precise nature of the supportive microenvironment remains largely unexplored. To address this question, we designed a laser microdissection-based approach to isolate the dorsal and ventral tissues of the aorta at three distinct developmental stages harboring HSPCs.

Read the full summary ↓

Bulk and single cell transcriptomics combined with computational analyses disclosed a large mesenchymal cell population in the E11.5 subaortic tissue including a subset expressing interconnected genes implicated in adhesive and neuronal functions. In vivo lineage tracing showed that this subset does not derive from neural crest cells. Histological and functional studies validated our strategy and revealed that Decorin, and Tenascin C, two components of the extracellular matrix (ECM), are essential for HSPC development. Together, our study identifies a yet unrecognized subaortic mesenchymal cell population and underscores the critical role of the ECM on embryonic HSPCs.

Published in

A multistep computational approach reveals a neuro-mesenchymal cell population in the embryonic hematopoietic stem cell niche

Miladinovic O, Canto PY, Pouget C et al. · Development (Cambridge, England) 2024 · PMID 38451068 · doi:10.1242/dev.202614

This dataset

Open GSE239434 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 GSE239434_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 PRJNA999307 and SRA study SRP451792. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38451068) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 2 more — browse all 2 samples with per-sample file links →

Datasets on a similar topic

GSE294951 GABA produced by multiple bone marrow niche cell types regulate hematopoietic stem and progenitor cells 12 samples shares hematopoietic, niche, stem
GSE293137 The bone marrow niche and hematopoietic system are distinctly remodeled by CD45-targeted astatine-211 radioimmunotherapy 14 samples shares hematopoietic, niche, stem
GSE265909 yHSC and oHSC scRNAseq with oHSC AThi ATlo Index Sorting. Assessing the transcriptional changes associated with autophagy engagement in old hematopoietic stem cells at single cell resolution. [scRNA-Seq] 563 samples shares hematopoietic, stem
GSE165881 Establishment of hematopoietic stem cell compartment after single cell transplantation tracked by FIT approach 62 samples shares hematopoietic, stem
GSE266509 A Bcl11a-driven mechanism maintaining hematopoietic stem cell functionality gives rise to dysfunction during aging [RNA-Seq] 52 samples shares hematopoietic, stem
GSE278208 STING Mediates Increased Self-Renewal and Lineage Skewing in DNMT3A-Mutated Hematopoietic Stem/Progenitor Cells 40 samples shares hematopoietic, stem
GSE267161 In Fanconi Anemia, impaired accumulation of bone marrow neutrophils during emergency granulopoiesis induces hematopoietic stem cell stress 38 samples shares hematopoietic, stem
GSE274033 RNA-seq of sorted murine long-term hematopoietic stem cells segmented on CUX1 levels with and without CUX1 knockdown 35 samples shares hematopoietic, stem

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.