SOX2 Drives Esophageal Squamous Carcinoma by Reprogramming Lipid Metabolism and Histone Acetylation Landscape
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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)
- Topic
- Esophageal cancerThis series is part of our curated briefing on it.
- Samples
- 16 samples: 12 distinct titles, 2 of them repeatedGroups 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
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 GSE256475_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 PRJNA1079746 and SRA study SRP491390. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 16 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.
- 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
- GSM8099027 KYSE450, shVec, rep1
- GSM8099028 KYSE450, shVec, rep2
- GSM8099029 KYSE450, shVec, rep3
- GSM8099030 KYSE450, shSOX2, rep1
- GSM8099031 KYSE450, shSOX2, rep2
- GSM8099032 KYSE450, shSOX2, rep3
- GSE180791 Proteogenomic characterization reveals that lipid droplet formation promotes esophageal squamous cell cancer progression 102 samples same disease briefing · shares esophageal, squamous, lipid
- GSE160269 Dissecting esophageal squamous-cell carcinoma ecosystem by single-cell transcriptomic analysis 128 samples same disease briefing · shares esophageal, squamous
- GSE20347 Analysis of gene expression in esophageal squamous cell carcinoma (ESCC) 34 samples same disease briefing · shares esophageal, squamous
- GSE185617 Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis 24 samples same disease briefing · shares esophageal, squamous
- GSE203067 Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Esophageal Squamous Cell Carcinoma 21 samples same disease briefing · shares esophageal, squamous
- GSE182090 RNA-sequencing assay to Identify Genes Promoting Lung Metastasis of Esophageal Squamous Cell Carcinoma (ESCC) Cells 12 samples same disease briefing · shares esophageal, squamous
- GSE201404 Ivermectin inhibits the growth of esophageal squamous cell carcinoma by activating ATF4-mediated endoplasmic reticulum stress-autophagy pathway 10 samples same disease briefing · shares esophageal, squamous
- GSE169337 Identification of differentially expressed genes in cisplatin-resistant and parental esophageal squamous cell carcinoma cells 8 samples same disease briefing · shares esophageal, squamous
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.