Gene expression profile at single cell level of cells isolated from the bone fracture gap and un-injured bone marrow in mouse osteotomy models
Single-cell RNA-seq · mouse · 15 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
- 15 samples: 15 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
- Erythroid precursors regulate local oxygen tension and repair outcomes in the bone marrow nichebioRxiv : the preprint server for biology · 2025
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE230260_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA958141 and SRA study SRP433736. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 15 sample titles: 15 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.
- GSM7210916 S1 Contralateral bone marrow, sample 1, External fixation rigid, Isotype control, scRNAseq
- GSM7210917 S1 Fracture gap, sample 1, External fixation rigid, Isotype control, scRNAseq
- GSM7210918 S2 Fracture gap, sample 2, External fixation rigid, Cd71 antibody, scRNAseq
- GSM7210919 S5 Contralateral bone marrow, sample 5, External fixation rigid, Isotype control, scRNAseq
- GSM7210920 S5 Fracture gap, sample 5, External fixation rigid, Isotype control, scRNAseq
- GSM7210921 S6 Fracture gap, sample 6, External fixation rigid, Cd71 antibody, scRNAseq
- GSM7210922 S7 and S8, Fracture gap, sample 7/8, External fixation compliant, isotype control, scRNAseq
- GSM7210923 S9 and S10, Fracture gap, sample 9/10, External fixation compliant, Cd71 antibody, scRNAseq
- GSM7210924 S11 Contralateral bone marrow, sample 11, External fixation rigid, Isotype control, scRNAseq
- GSM7210925 S11 Fracture gap, sample 11, External fixation rigid, Isotype control, scRNAseq
- GSM7210926 S12 Fracture gap, sample 12, External fixation rigid, Cd71 antibody, scRNAseq
- GSM7210927 S13 and S14, Fracture gap, sample 13/14, External fixation compliant, isotype control, scRNAseq
- GSM7210928 S15 and S16, Fracture gap, sample 15/16, External fixation compliant, isotype control, scRNAseq
- GSM7210929 S17 and S18, Fracture gap, sample 17/18, External fixation compliant, isotype control, scRNAseq
- GSM7210930 S19 and S20, Fracture gap, sample 19/20, External fixation compliant, isotype control, scRNAseq
- 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 isolated, marrow, level, bone
- 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 isolated, marrow, level, bone
- GSE268240 Gene expression profiling of neutrophils isolated from bone marrow, spleen and tumor of H16sc-IS1-tumor-bearing mice treated with anti-IL1RAP or untreated. 24 samples shares isolated, marrow, bone
- GSE313387 Brain-Engrafted Monocyte-derived Macrophages from Blood and Skull-Bone Marrow Exhibit Distinct Properties [bulkRNA_isolatedBrainParenchymalMacrophages] 18 samples shares isolated, marrow, bone
- GSE284186 Gene expression profile at single cell level of hepatocytes and non parenchymal cells (NPCs) isolated from a murine model of MASLD 8 samples shares isolated, level
- GSE246844 gene expression profile of lung immune cells isolated from mock- or SARS-CoV-2 infected mice at single cell level 4 samples shares isolated, level
- GSE327960 Transcription profiles of mouse microglia isolated by FACS from WT and Grn KO animals, separated by lipofuscin levels [hex001110] 24 samples shares isolated, level
- GSE273792 Multimodal single cell profiling of bone fracture microenvironment 24 samples shares fracture, bone
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.