Macrophages suppress cardiac reprogramming of fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuit
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 11 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 11 samples: 2 × In vivo-1w vs 2 × In vitro-1w vs 2 × In vivo-2w vs 2 × In vitro-2wGroups 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
- Macrophages suppress cardiac reprogramming of fibroblasts in vivo via IFN-mediated intercellular self-stimulating circuitProtein & cell · 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 GSE261309_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1086461 and SRA study SRP494519. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 8 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.
- GSM8140346 In vivo-1w-1 In vivo-1w
- GSM8140347 In vivo-1w-2 In vivo-1w
- GSM8140348 In vitro-1w-1 In vitro-1w
- GSM8140349 In vitro-1w-2 In vitro-1w
- GSM8140350 In vivo-2w-1 In vivo-2w
- GSM8140351 In vivo-2w-2 In vivo-2w
- GSM8140352 In vitro-2w-1 In vitro-2w
- GSM8140353 In vitro-2w-2 In vitro-2w
- GSM8140354 control
- GSM8140355 shIfnar2
- GSM8140356 STAT1-i
- GSE22292 Gene expression in mouse neonatal cardiomyocytes, cardiac fibroblasts, reprogramming failed GFP- cells, and GFP+ iCMs 18 samples shares reprogramming, fibroblasts, cardiac
- GSE267452 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming 54 samples shares reprogramming, cardiac
- GSE295779 The whole-genome duplication is a barrier for iPSCs reprogramming from mouse fibroblasts 28 samples shares reprogramming, fibroblasts
- GSE282695 STAT3 regulates pathogen control and clearance in macrophages by reprogramming inflammation-induced microbial defense response 18 samples shares reprogramming, macrophages
- GSE218761 Cardiac reprogramming and Gata4 overexpression reduce fibrosis and improve diastolic dysfunction in heart failure with preserved ejection fraction 18 samples shares reprogramming, cardiac
- GSE305170 Maintenance of Fibroblast Identity During Cardiac Reprogramming and Heart Repair [RNA-seq] 18 samples shares reprogramming, cardiac
- GSE261139 Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential 16 samples shares reprogramming, macrophages
- GSE267447 Loss of Nuclear Receptor Nr4a3 Alleviates Cellular Senescence to Promote Adult Direct Cardiac Reprogramming (ATAC-Seq) 16 samples shares reprogramming, 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.