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Transcriptomic profiling of ZR-75-1 wild-type and RB1 knockout cells treated with abemaciclib

GSE336741 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/06/29 Platform GPL30173
At a glance

RNA-seq (gene expression) · human · 12 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
Breast cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × ZR751 sgControl DMSO RNAseq vs 3 × ZR751 sgControl Abemaciclib RNAseq vs 3 × ZR751 RB1 KO DMSO RNAseq vs 3 × ZR751 RB1 KO Abemaciclib RNAseqGroups 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)
The retinoblastoma protein (Rb) is a tumour suppressor best known for repressing E2F transcription factors and halting cell cycle progression. In hormone receptor-positive breast cancer, CDK4/6 inhibitors activate Rb by preventing its phosphorylation, forming a key component of current endocrine therapy regimens. How pharmacologically activated Rb remodels chromatin and influences transcriptional networks beyond cell cycle arrest remains poorly understood.
Read the full summary ↓
Here, we validated the specificity of the Rb antibody for CUT&RUN, and measured changes in Rb chromatin binding after treatment with abemaciclib. We show that CDK4/6 inhibition induces widespread redistribution of Rb to both promoters and enhancers in cancer cells. While Rb predictably binds to cell cycle gene promoters where it represses transcription, at other sites it unexpectedly promotes expression of oestrogen-responsive genes by integrating into oestrogen receptor (ER)-rich transcriptional hubs. This reprogramming is mediated in part by KDM5A and KDM5B, whose functional interaction with Rb contributes to transcriptional regulation at these loci. In patient-derived models and clinical samples of endocrine-sensitive breast cancer, CDK4/6 inhibition enhances ER target gene expression, sensitising tumours to anti-oestrogen therapy. However, in endocrine-resistant contexts – such as ESR1-mutant breast cancer – this Rb-driven oestrogenic programme serves to limit therapeutic efficacy. These findings reframe Rb as a dual-function transcriptional regulator – one that enforces cell cycle arrest while driving transcriptional programs with important therapeutic implications. This expanded model of Rb function provides a new mechanistic basis for the synergy between CDK4/6 inhibitors and endocrine therapy, and offers insight into resistance mechanisms in hormone receptor-positive breast cancer.
This dataset
Open GSE336741 in finder → Find more human RNA-seq datasets → Breast 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 GSE336741_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1482482 and SRA study SRP712916. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × ZR751 sgControl DMSO RNAseq vs 3 × ZR751 sgControl Abemaciclib RNAseq vs 3 × ZR751 RB1 KO DMSO RNAseq vs 3 × ZR751 RB1 KO Abemaciclib RNAseq

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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 Breast cancer datasets

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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.