PAX3-SIX2 muscle stem cell heterogeneity drives muscle-specific repair dynamics diversification
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. 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
- 12 samples: 3 × GFP_neg_CTR_plasmid vs 3 × GFP_neg_SIX2_plasmid vs 3 × GFP_pos_CTR_plasmid vs 3 × GFP_pos_SIX2_plasmidGroups 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.
Read the full summary ↓
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 GSE325703_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 PRJNA1441483 and SRA study SRP685944. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 of them. 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.
- GSM9610946 GFP_neg_CTR_plasmid_rep1 GFP_neg_CTR_plasmid
- GSM9610947 GFP_neg_CTR_plasmid_rep2 GFP_neg_CTR_plasmid
- GSM9610948 GFP_neg_CTR_plasmid_rep3 GFP_neg_CTR_plasmid
- GSM9610949 GFP_neg_SIX2_plasmid_rep1 GFP_neg_SIX2_plasmid
- GSM9610950 GFP_neg_SIX2_plasmid_rep2 GFP_neg_SIX2_plasmid
- GSM9610951 GFP_neg_SIX2_plasmid_rep3 GFP_neg_SIX2_plasmid
- GSM9610952 GFP_pos_CTR_plasmid_rep1 GFP_pos_CTR_plasmid
- GSM9610953 GFP_pos_CTR_plasmid_rep2 GFP_pos_CTR_plasmid
- GSM9610954 GFP_pos_CTR_plasmid_rep3 GFP_pos_CTR_plasmid
- GSM9610955 GFP_pos_SIX2_plasmid_rep1 GFP_pos_SIX2_plasmid
- GSM9610956 GFP_pos_SIX2_plasmid_rep2 GFP_pos_SIX2_plasmid
- GSM9610957 GFP_pos_SIX2_plasmid_rep3 GFP_pos_SIX2_plasmid
- GSE313732 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [RNA-Seq] 78 samples shares heterogeneity, dynamics
- GSE232957 Muscle-specific rescue of Bmal1 impacts survival and health span of the Bmal1-KO mouse 72 samples shares muscle-specific, muscle
- GSE263106 Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle 36 samples shares muscle-specific, muscle
- GSE325974 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [day0 RNA-Seq] 20 samples shares heterogeneity, dynamics
- GSE313167 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [ICAM1 RNAseq] 19 samples shares heterogeneity, dynamics
- GSE263105 Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle in 18 months-old mice 14 samples shares muscle-specific, muscle
- GSE263104 Effect of muscle-specific Pex5 depletion on gene expression in gastrocnemius muscle in 9 months-old mice 13 samples shares muscle-specific, muscle
- GSE313164 Type I IFN Dynamics Orchestrate Protective ICAM1⁺ Neutrophil Heterogeneity as an Early Checkpoint for Survival in Lethal Viral Infection [BM RNAseq] 12 samples shares heterogeneity, dynamics
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.