Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architecture
RNA-seq (gene expression) · mouse · 10 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 10 samples: 10 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
- Spatiotemporal transcriptomic mapping of regenerative inflammation in skeletal muscle reveals a dynamic multilayered tissue architectureThe Journal of clinical investigation · 2024
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 GSE223813_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA928448 and SRA study SRP419868. 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 10 sample titles: 10 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.
- GSM6996255 Day 1 after CTX muscle injury (scRNA-seq)
- GSM6996256 Day 2 after CTX muscle injury (scRNA-seq)
- GSM6996257 2 month old D2.mdx mouse (scRNA-seq)
- GSM6996258 C57 Day 4 after CTX muscle injury (stRNA-seq)
- GSM6996259 C57 Day 8 after CTX muscle injury (stRNA-seq)
- GSM6996260 DBA2/J Day 8 after CTX muscle injury (stRNA-seq)
- GSM6996261 2 month old D2.mdx mouse (Rep1) (stRNA-seq)
- GSM6996262 2 month old D2.mdx mouse (Rep2) (stRNA-seq)
- GSM6996263 2 month old D2.mdx mouse treated weekly (Q.W.) with Prednisone starting at 1 month old (Rep1) (stRNA-seq)
- GSM6996264 2 month old D2.mdx mouse treated weekly (Q.W.) with Prednisone starting at 1 month old (Rep2) (stRNA-seq)
- GSE318627 Physiomimetic 3D skeletal muscle reveals senescence-driven matreotype remodeling driving paracrine senescence and regenerative failure 9 samples shares regenerative, skeletal, muscle
- GSE308859 Integrated Spatial Transcriptomics and Single-Cell RNA Sequencing Reveal Lars2-Mediated Spatiotemporal Dynamics of Myocardial Remodeling in a Mouse Model of Transverse Aortic Constriction (TAC) 8 samples shares spatiotemporal, dynamic
- GSE284137 Tissue and cellular spatiotemporal dynamics in colon aging 395 samples shares spatiotemporal, dynamic
- GSE341480 Spatiotemporal Clonal Architecture of the Newborn Mouse Forebrain 186 samples shares spatiotemporal, architecture
- GSE200114 Dynamic promoter-enhancer contacts contribute to spatiotemporal gene expression during mouse fetal development 70 samples shares spatiotemporal, dynamic
- GSE280373 Spatiotemporal dynamics of the cardioimmune niche during lesion repair [scRNA-seq] 28 samples shares spatiotemporal, dynamic
- GSE286877 Chaperone-mediated autophagy sustains muscle stem cell regenerative functions but declines with age 24 samples shares regenerative, muscle
- GSE285985 Tissue and cellular spatiotemporal dynamics in colon aging [scRNA-seq] 23 samples shares spatiotemporal, dynamic
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.