Single cell transcriptomic analyses of the dynamic local and systemic response to cardiac injury in mice and zebrafish
Single-cell RNA-seq · zebrafish · 52 samples
- What it is
- Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
- Organism
- Danio rerio (zebrafish)
- Samples
- 52 samples: 40 distinct titles, 12 of them repeatedGroups 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
- Cross-species single-cell RNA-seq analysis reveals disparate and conserved cardiac and extracardiac inflammatory responses upon heart injuryCommunications biology · 2024
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 GSE227191_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 PRJNA943547 and SRA study SRP426909. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 52 sample titles: 40 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.
- GSM7092908 Blood 1dpi MI
- GSM7092909 Blood 1dpi SH
- GSM7092910 Heart 1dpi, MI
- GSM7092911 Heart 1dpi SH
- GSM7092912 Pancreatic Islets 1dpi MI
- GSM7092913 Pancreatic Islets 1dpi SH
- GSM7092914 Liver 1dpi MI
- GSM7092915 Liver 1dpi SH
- GSM7092916 Heart 30dpi MI
- GSM7092917 Heart 30dpi SH
- GSM7092918 Kidney 30dpi SH
- GSM7092919 Kidney 30dpi MI
- GSM7092920 Liver 30dpi MI
- GSM7092921 Liver 30dpi SH
- GSM7092922 Blood 7dpi MI
- GSM7092923 Blood 7dpi SH
- GSM7092924 Heart 7dpi MI
- GSM7092925 Heart 7dpi SH
- GSM7092926 Kidney 7dpi SH
- GSM7092927 Kidney 7dpi MI
- GSM7092928 Liver 7dpi MI
- GSM7092929 Liver 7dpi SH
- GSM7092930 Blood 30dpi MI
- GSM7092931 Blood 30dpi SH
- GSM7092932 Pancreatic Islets 30dpi MI
- GSM7092933 Pancreatic Islets 30dpi SH
- GSM7092934 Pancreatic Islets 7dpi MI
- GSM7092935 Pancreatic Islets 7dpi SH
- GSM7092936 heart 1 dpi replicate 1
- GSM7092937 heart 1 dpi replicate 2
- GSM7092938 liver 1 dpi replicate 1
- GSM7092939 liver 1 dpi replicate 2
- GSM7092940 Pancreas 1 dpi replicate 1
- GSM7092941 Pancreas 1 dpi replicate 2
- GSM7092942 WKM 1 dpi replicate 1
- GSM7092943 WKM 1 dpi replicate 2
- GSM7092944 heart 7 dpi replicate 1
- GSM7092945 heart 7 dpi replicate 2
- GSM7092946 liver 7 dpi replicate 1
- GSM7092947 liver 7 dpi replicate 2
+ 12 more — browse all 52 samples with per-sample file links →
- GSE241156 Interspecies comparison reveals Hmga1 as driver of cardiac regeneration [TOMOseq mouse and zebrafish] 14 samples shares zebrafish, cardiac
- GSE227670 The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue 18 samples shares zebrafish
- GSE185283 Time-resolved RNA sequencing reveals distinct post-transcriptional regimes during zebrafish embryogenesis 72 samples shares zebrafish
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.