GEO series

Redirecting the pioneering function of FOXA1 with covalent small molecules [ChIP-seq]

GSE261803 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 15 samples Submitted 2024/03/26 Platform GPL30173

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 15 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: 15 samples: 15 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.

Summary (written by the submitters)

Pioneer transcription factors (TFs) exhibit a special ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain.

Read the full summary ↓

We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.

This dataset

Open GSE261803 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

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 GSE261803_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 PRJNA1089117 and SRA study SRP496070. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

15 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 15 sample titles: 15 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.

Samples in this study

GSM8152261 22Rv1-parental, Input
GSM8152262 22Rv1-parental, DMSO, FOXA1
GSM8152263 22Rv1-parental, PladB, FOXA1
GSM8152264 22Rv1-parental, WX-02-23, FOXA1
GSM8152265 22Rv1-parental, WX-02-43, FOXA1
GSM8152266 22Rv1-parental, siFOXA1, FOXA1
GSM8152267 22Rv1-parental, si-control, FOXA1
GSM8152268 22Rv1-FOXA1-WT, Input
GSM8152269 22Rv1-FOXA1-WT, noDox, FOXA1
GSM8152270 22Rv1-FOXA1-WT, DMSO, FOXA1
GSM8152271 22Rv1-FOXA1-WT, WX-02-23, FOXA1
GSM8152272 22Rv1-FOXA1-C258A, Input
GSM8152273 22Rv1-FOXA1-C258A, noDox, FOXA1
GSM8152274 22Rv1-FOXA1-C258A, DMSO, FOXA1
GSM8152275 22Rv1-FOXA1-C258A, WX-02-23, FOXA1

Datasets on a similar topic

GSE261801 Redirecting the pioneering function of FOXA1 with covalent small molecules [ATAC-seq] 29 samples shares foxa1, redirecting, pioneering, molecules, covalent, small
GSE273817 Redirecting the pioneering function of FOXA1 with covalent small molecules [ATAC-Seq] 9 samples shares foxa1, redirecting, pioneering, molecules, covalent, small
GSE273816 Redirecting the pioneering function of FOXA1 with covalent small molecules 12 samples shares foxa1, redirecting, pioneering, molecules, covalent, small
GSE290894 Rewiring the fusion oncoprotein EWSR1::FLI1 in Ewing scarcoma with bivalent small molecules [ChIP-Seq] 24 samples shares molecules, chip-seq, small
GSE245967 EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells (ChIP-seq) 90 samples shares foxa1, chip-seq
GSE281784 Targeting FOXA1 and FOXA2 Disrupts the Lineage-Specific Oncogenic Output in Prostate Cancer [ChIP-seq] 67 samples shares foxa1, chip-seq
GSE285790 KMT2D promotes castration-resistant prostate cancer progerssion by reactivating AR via FOXA1 [ChIP-seq, Cut & Tag] 48 samples shares foxa1, chip-seq
GSE305432 FOXA1/FOXM1 ChIP-seq on giredestrant-resistant ER+ breast cancer cell lines 20 samples shares foxa1, chip-seq

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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