SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape (ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- Homo sapiens (human)
- Samples
- 10 samples: 10 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
- SOX2 drives esophageal squamous carcinoma by reprogramming lipid metabolism and histone acetylation landscapeNature communications · 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 GSE256473_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 PRJNA1079751 and SRA study SRP491390. 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 10 sample titles: 10 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.
- GSM8099017 KYSE450, WT, SOX2,ChIP
- GSM8099018 KYSE450, WT, H3K4me3,ChIP
- GSM8099019 KYSE450, WT, H3K27ac,ChIP
- GSM8099020 KYSE450, WT, H4ac,ChIP
- GSM8099021 KYSE450, shSOX2, SOX2,ChIP
- GSM8099022 KYSE450, shSOX2, H3K4me3,ChIP
- GSM8099023 KYSE450, shSOX2, H3K27ac,ChIP
- GSM8099024 KYSE450, shSOX2, H4ac,ChIP
- GSM8099025 KYSE450, WT, ChIP input
- GSM8099026 KYSE450, shSOX2, ChIP input
- GSE286492 CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks 38 samples shares acetylation, chip-seq, histone
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares reprogramming, chip-seq
- GSE307716 Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [CUT&Tag] 52 samples shares acetylation, histone
- GSE206726 Epigenetic reprogramming of the mesenchymal state by SUV39H1/H2 [ChIP-Seq] 42 samples shares reprogramming, chip-seq
- GSE311971 Regulation of lineage reprogramming by dynamic chromatin SUMOylation (ChIP-seq) 41 samples shares reprogramming, chip-seq
- GSE261321 NF-κB- and TET2-mediated macrophage reprogramming overrides the anti-inflammatory effects of hypoxia and improves responses in human cancer ChIP-Seq). 24 samples shares reprogramming, chip-seq
- GSE308983 Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ChIP-Seq] 23 samples shares reprogramming, chip-seq
- GSE301553 The impact of Fulvestrant on Estrogen Receptor-Driven Chromatin Dynamics in breast cancer cells points to a disconnect between chromatin opening and histone acetylation [CUT&Tag] 18 samples shares acetylation, histone
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.