GEO series

Single-cell transcriptomic profiling of c-Kit⁺ HSPCs in a KrasG12D/+ mouse model of JMML

GSE313553 Mus musculus (mouse) Single-cell RNA-seq 2 samples Submitted 2026/03/31 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.
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.

Summary (written by the submitters)

We performed single-cell RNA sequencing (scRNA-seq) to characterize hematopoietic stem and progenitor cells (HSPCs) in a KrasG12D/+ mouse model of juvenile myelomonocytic leukemia (JMML). C-Kit⁺ HSPCs were enriched from the bone marrow of 6-week-old KrasG12D/+ and wild-type (WT) mice using CD117 MicroBeads and processed using the 10x Genomics Chromium Single Cell 3′ v3 platform.

Read the full summary ↓

Libraries were sequenced on an Illumina NovaSeq 6000 system. Raw data were processed with Cell Ranger and analyzed using Seurat for quality control, dimensionality reduction, and clustering. HSPC subsets, developmental trajectories, and pathway activities were then analyzed to characterize leukemic alterations.

This dataset

Open GSE313553 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 GSE313553_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 PRJNA1380309 and SRA study SRP654748. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

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

GSE269680 CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial) 15 samples shares krasg12d
GSE192687 Single-cell RNAseq analysis of renal endothelial cells in murine diabetic nephropathy 5464 samples shares single-cell
GSE290574 Gene Regulatory Networks Orchestrating Oocyte Fate Bifurcation in Primordial Follicles Revealed by Single-Cell Transcriptomics 386 samples shares single-cell
GSE327176 Single-cell transcriptomic profiling unveils tumor-mediated reprogramming of neutrophils and their unique vulnerability that inhibits metastasis 25 samples shares single-cell
GSE276088 Single-cell transcriptomic and spatial subcellular landscape of the articular disk synovium in mouse temporomandibular joint osteoarthritis 18 samples shares single-cell
GSE277789 Spatiotemporal and genetic cell lineage tracing of endodermal organogenesis at single-cell resolution [Smart-seq3-RNA-seq-add] 830 samples shares single-cell
GSE239602 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 82 samples shares single-cell
GSE315482 Single-Cell Multi-omics Profiling of Mouse Hepatic Immune Microenvironment Reveals Neutrophil-Kupffer Cell Crosstalk via Thrombospondin-1/CD36 after Surgical Stress 10 samples shares single-cell

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.