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Characterization of E2F8-mediated transcriptional regulation in lethal prostate cancer

GSE275631 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 39 samples Submitted 2025/01/10 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 39 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
Prostate cancerThis series is part of our curated briefing on it.
Samples
39 samples: 8 conditions, mostly in triplicateGroups 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
Integrative analysis identifies the atypical repressor E2F8 as a targetable transcriptional activator driving lethal prostate cancerOncogene · 2025
Summary (written by the submitters)
To identify the genomic bindings and transcriptional targets of E2F8 in lethal prostate cancer cells. To examine the potential off-target effects by CRISPR/CasRx-mediated E2F8 knockdown in 293FT cells. To analyze differentially expressed genes upon TT3 LLN-CRISPR/CasRx-mediated E2F8 knockdown in DU145 xenografts.
Published in
Integrative analysis identifies the atypical repressor E2F8 as a targetable transcriptional activator driving lethal prostate cancer
Huang F, Li K, Chen Z et al. · Oncogene 2025 · PMID 39613933 · doi:10.1038/s41388-024-03239-2
This dataset
Open GSE275631 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Prostate cancer landscape →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE275631_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1152279 and SRA study SRP528595. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39613933) ↗
Study design
8 conditions, mostly in triplicate
DU145 xeno_TT3 LLN-CasRx/pre-gCtrl ×6 PC3_IgG ChIP ×3 PC3_E2F8 ChIP ×3 DU145_IgG ChIP ×3 DU145_E2F8 ChIP ×3 293FT_pre-gCtrl ×3 293FT_pre-gE2F8 ×3 DU145 xeno_TT3 LLN-CasRx/pre-gE2F8 ×3 +12 more

Supports a between-group comparison across 27 samples.

How we read this: 8 replicated groups read from 39 sample titles; they account for 27 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.

Samples in this study
More Prostate cancer datasets

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