Chromatin-immunoprecipitation followed by sequencing (ChIPseq) of SOX17 and FOXA2 in yolk-sac tumor cell lines
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)
- Samples
- 16 samples: 16 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
- Induction of SOX17 with stimulation of WNT, TGF-beta, and FGF signaling drives embryonal carcinomas into the yolk-sac tumor lineage resulting in increased cisplatin resistanceInternational journal of cancer · 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 GSE276475_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 PRJNA1157437 and SRA study SRP530772. 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 16 sample titles: 16 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.
- GSM8499172 GCT72-input_I
- GSM8499173 GCT72-input_II
- GSM8499174 GCT72-SOX17_I
- GSM8499175 GCT72-SOX17_II
- GSM8499176 GCT72-SOX17_III
- GSM8499177 GCT72-FOXA2_I
- GSM8499178 GCT72-FOXA2_II
- GSM8499179 GCT72-FOXA2_III
- GSM8499180 1411H-input_I
- GSM8499181 1411H-input_II
- GSM8499182 1411H-SOX17_I
- GSM8499183 1411H-SOX17_II
- GSM8499184 1411H-SOX17_III
- GSM8499185 1411H-FOXA2_I
- GSM8499186 1411H-FOXA2_II
- GSM8499187 1411H-FOXA2_III
- GSE312323 Identification of genomic features that uniquely impact estrogen receptor alpha binding and its effects on gene expression in endometrial cancer [SOX17_ChIPseq] 2 samples shares sox17, chipseq
- GSE281525 RNA-sequence data of clinically never-metastatic primary small cell lung cancer cases and small cell lung cancer metastasis cases, FOXA2 knock-down and overexpression in cell lines 61 samples shares foxa2, lines
- GSE301056 Chromatin Isolation by RNA purification (ChIRP)-followed RNA sequencing of human leukemia cell lines, MOLMO13 and OCI-AML4, folowing lncRNA CRISPR/Cas9 editing and cytosine base editing 8 samples shares followed, lines
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares foxa2
- GSE281784 Targeting FOXA1 and FOXA2 Disrupts the Lineage-Specific Oncogenic Output in Prostate Cancer [ChIP-seq] 67 samples shares foxa2
- GSE210081 Identification of H3K27ac marks influenced by FOXA2 and/or mutant KRAS in BEAS-2B transformed human bronchial epithelial cells 16 samples shares foxa2
- GSE232553 FOXA2/AP-1 drives prostate cancer lineage plasticity [PDX ChIP-seq] 16 samples shares foxa2
- GSE239269 Investigate FOXA2 regulated chromatin state program during NEPC transformation by ATAC-seq. 12 samples shares foxa2
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.