Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivo
RNA-seq (gene expression) · mouse · 15 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
- 15 samples: 5 conditions, mostly in triplicateGroups 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
- Perturb-seq uncovers pathological obstacles to direct cardiac reprogramming in vivoCell stem cell · 2026
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 GSE305453_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 PRJNA1306002 and SRA study SRP608910. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM9177273 MICF_0w_1 MICF_0w
- GSM9177274 MICF_0w_2 MICF_0w
- GSM9177275 MICF_0w_3 MICF_0w
- GSM9177276 shCalr_1w_1 shCalr_1w
- GSM9177277 shCalr_1w_2 shCalr_1w
- GSM9177278 shCalr_1w_3 shCalr_1w
- GSM9177279 shCalr_2w_1 shCalr_2w
- GSM9177280 shCalr_2w_2 shCalr_2w
- GSM9177281 shCalr_2w_3 shCalr_2w
- GSM9177282 shNT_1w_1 shNT_1w
- GSM9177283 shNT_1w_2 shNT_1w
- GSM9177284 shNT_1w_3 shNT_1w
- GSM9177285 shNT_2w_1 shNT_2w
- GSM9177286 shNT_2w_2 shNT_2w
- GSM9177287 shNT_2w_3 shNT_2w
- GSE267452 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming 54 samples shares reprogramming, cardiac, direct
- GSE267447 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (ATAC-Seq) 16 samples shares reprogramming, cardiac, direct
- GSE239602 Single-cell and spatial transcriptomics uncovers the role of senescent vascular cells in pathological arterial remodeling during murine atherosclerosis 82 samples shares pathological, uncovers
- GSE270509 In vivo CRISPR screen reveals interplay of epigenetic regulators underlies kinetics of hepatobiliary reprogramming [RNA-Seq] 27 samples shares reprogramming, vivo
- GSE300625 In vivo chemical reprogramming is associated with a toxic accumulation of lipid droplets hindering rejuvenation 20 samples shares reprogramming, vivo
- GSE305170 Maintenance of Fibroblast Identity During Cardiac Reprogramming and Heart Repair [RNA-seq] 18 samples shares reprogramming, cardiac
- GSE261561 Contribution of VEGF-B-induced endocardial endothelial cell lineage in physiological versus pathological cardiac hypertrophy. 12 samples shares pathological, cardiac
- GSE307584 Aberrant Upregulation of Histamine N-Methyltransferase Exacerbates Pathological Cardiac Hypertrophy and Heart Failure via Disruption of SAM/Frizzled-2/ CaMKII Signaling Pathway [RNA-seq] 12 samples shares pathological, cardiac
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.