Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE MEF/4in1 ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 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
- Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesisNature genetics · 2025
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 GSE224825_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 PRJNA934517 and SRA study SRP424218. 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 12 sample titles: 12 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.
- GSM7033675 MEF day02 rep1 [ATAC-seq]
- GSM7033676 MEF day02 rep2 [ATAC-seq]
- GSM7033677 MEF day02 rep3 [ATAC-seq]
- GSM7033678 Prox1_OE day02 rep1 [ATAC-seq]
- GSM7033679 Prox1_OE day02 rep2 [ATAC-seq]
- GSM7033680 Prox1_OE day02 rep3 [ATAC-seq]
- GSM7033681 4in1_GFP_OE day02 rep1 [ATAC-seq]
- GSM7033682 4in1_GFP_OE day02 rep2 [ATAC-seq]
- GSM7033683 4in1_GFP_OE day02 rep3 [ATAC-seq]
- GSM7033684 4in1_Prox1_OE day02 rep1 [ATAC-seq]
- GSM7033685 4in1_Prox1_OE day02 rep2 [ATAC-seq]
- GSM7033686 4in1_Prox1_OE day02 rep3 [ATAC-seq]
- GSE224831 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE iHep Timecourse RNA-seq] 16 samples shares prox1, tumorigenesis, repression, plasticity, safeguards, hepatocyte
- GSE224830 Active repression of cell fate plasticity by PROX1 safeguards hepatocyte identity and prevents liver tumorigenesis [Prox1 OE iHep Timecourse scRNA-seq] 13 samples shares prox1, tumorigenesis, repression, plasticity, safeguards, hepatocyte
- GSE295582 Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_H2AX_gH2AX_MEF] 24 samples shares mef, safeguards
- GSE295584 Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [ChIP_SIRT7_MEF] 12 samples shares mef, safeguards
- GSE278097 Remodeling of tissue-resident macrophages by MEF2D-expressing cancer precursors primes for liver tumorigenesis [RNA-Seq] 17 samples shares mef, tumorigenesis
- GSE280084 A Multipotent PROX1+ Tumor Cell Population Emerges During Intestinal Tumorigenesis and Mediates Radioresistance in Colorectal Cancer 13 samples shares prox1, tumorigenesis
- GSE295586 Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome [RNA-seq_male_female_MEF] 12 samples shares mef, safeguards
- GSE280834 Divergently evolved FOXA1 mutations drive prostate tumorigenesis or therapy-resistant intra-luminal plasticity [ChIP-seq] 17 samples shares tumorigenesis, plasticity
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.