Sox4 is a master regulator of epithelial-mesenchymal transition (EMT) by controlling Ezh2 expression and epigenetic reprogramming
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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
- 13 samples: 6 conditions, mostly in duplicateGroups 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.
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 GSE45579_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 PRJNA194616 and SRA study SRP020232. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 13 sample titles; they account for 12 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.
- GSM1110018 NMuMG_Input_DNA
- GSM1110019 NMuMG_day00_H3K27me3, biological replicate 1 NMuMG_day00_H3K27me3,
- GSM1110020 NMuMG_day00_H3K27me3, biological replicate 2 NMuMG_day00_H3K27me3,
- GSM1110021 NMuMG_day01_H3K27me3, biological replicate 1 NMuMG_day01_H3K27me3,
- GSM1110022 NMuMG_day01_H3K27me3, biological replicate 2 NMuMG_day01_H3K27me3,
- GSM1110023 NMuMG_day04_H3K27me3, biological replicate 1 NMuMG_day04_H3K27me3,
- GSM1110024 NMuMG_day04_H3K27me3, biological replicate 2 NMuMG_day04_H3K27me3,
- GSM1110025 NMuMG_day07_H3K27me3, biological replicate 1 NMuMG_day07_H3K27me3,
- GSM1110026 NMuMG_day07_H3K27me3, biological replicate 2 NMuMG_day07_H3K27me3,
- GSM1110027 NMuMG_day10_H3K27me3, biological replicate 1 NMuMG_day10_H3K27me3,
- GSM1110028 NMuMG_day10_H3K27me3, biological replicate 2 NMuMG_day10_H3K27me3,
- GSM1110029 NMuMG_day20_H3K27me3, biological replicate 1 NMuMG_day20_H3K27me3,
- GSM1110030 NMuMG_day20_H3K27me3, biological replicate 2 NMuMG_day20_H3K27me3,
- GSE254324 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [CUT&RUN] 14 samples shares ezh2, epigenetic
- GSE254328 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase 26 samples shares ezh2, epigenetic
- GSE288196 Single cell multiomics unravel the transcription networks controlling the different EMT tumor states [bulk RNA-seq] 22 samples shares emt, controlling
- GSE304090 Pharmacological inhibition of the epigenetic enzyme EZH2 attenuates cardiac dysfunction and mitigates lipid metabolism perturbations in a murine model of myocardial infarction 15 samples shares ezh2, epigenetic
- GSE254325 Epigenetic regulation of chromosomal instability by EZH2 methyltransferase [RNA-seq] 12 samples shares ezh2, epigenetic
- GSE334791 Effect of depletion of Nsd1 or Ezh2 on gene expression during pluripotency transition 8 samples shares ezh2, transition
- GSE280007 EZH2-mediated macrophage-to-myofibroblast transition contributes to calcium oxalate crystal-induced kidney fibrosis 6 samples shares ezh2, transition
- GSE288220 Single cell multiomics unravel the transcription networks controlling the different EMT tumor states [multiome] 6 samples shares emt, controlling
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.