GEO series

Multiome analysis of PDxOs (HCI-003, HCI-005, HCI-011) treated with a CDK4/6 inhibitor for 3 weeks

GSE338025 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 36 samples Submitted 2026/07/13 Platform GPL34281

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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: 36 samples: 36 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)

This study uses single-nucleus multiome profiling, as well as bulk methylation profiling, to characterize the transcriptional, chromatin accessibility, and DNA methylation changes after 3 weeks of CDK4/6 inhibitor treatment in organoids grown from patient-derived xenograft tumors (PDxOs) generated from 3 patients: HCI-003, HCI-005, and HCI-011.

This dataset

Open GSE338025 in finder → Find more human RNA-seq 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 GSE338025_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 PRJNA1492128 and SRA study SRP716426. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

36 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 36 sample titles: 36 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

GSM9864763 HCI-003, CDKi, MN87, mRNA
GSM9864764 HCI-003, CDKi, MN87, ATAC
GSM9864765 HCI-003, CDKi, MN87, RREMS
GSM9864766 HCI-003, DMSO, MN87, mRNA
GSM9864767 HCI-003, DMSO, MN87, ATAC
GSM9864768 HCI-003, DMSO, MN87, RREMS
GSM9864769 HCI-003, CDKi, MN93, mRNA
GSM9864770 HCI-003, CDKi, MN93, ATAC
GSM9864771 HCI-003, CDKi, MN93, RREMS
GSM9864772 HCI-003, DMSO, MN93, mRNA
GSM9864773 HCI-003, DMSO, MN93, ATAC
GSM9864774 HCI-003, DMSO, MN93, RREMS
GSM9864775 HCI-005, CDKi, MN93, mRNA
GSM9864776 HCI-005, CDKi, MN93, ATAC
GSM9864777 HCI-005, CDKi, MN93, RREMS
GSM9864778 HCI-005, DMSO, MN93, mRNA
GSM9864779 HCI-005, DMSO, MN93, ATAC
GSM9864780 HCI-005, DMSO, MN93, RREMS
GSM9864781 HCI-005, CDKi, MN94, mRNA
GSM9864782 HCI-005, CDKi, MN94, ATAC
GSM9864783 HCI-005, CDKi, MN94, RREMS
GSM9864784 HCI-005, DMSO, MN94, mRNA
GSM9864785 HCI-005, DMSO, MN94, ATAC
GSM9864786 HCI-005, DMSO, MN94, RREMS
GSM9864787 HCI-011, CDKi, MN87, mRNA
GSM9864788 HCI-011, CDKi, MN87, ATAC
GSM9864789 HCI-011, CDKi, MN87, RREMS
GSM9864790 HCI-011, DMSO, MN87, mRNA
GSM9864791 HCI-011, DMSO, MN87, ATAC
GSM9864792 HCI-011, DMSO, MN87, RREMS
GSM9864793 HCI-011, CDKi, MN93, mRNA
GSM9864794 HCI-011, CDKi, MN93, ATAC
GSM9864795 HCI-011, CDKi, MN93, RREMS
GSM9864796 HCI-011, DMSO, MN93, mRNA
GSM9864797 HCI-011, DMSO, MN93, ATAC
GSM9864798 HCI-011, DMSO, MN93, RREMS

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