GEO series

CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation

GSE295260 Homo sapiens (human) RNA-seq (gene expression) 40 samples Submitted 2026/06/29 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 40 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)
Samples: 40 samples: 40 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: CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activationLife science alliance · 2026

Summary (written by the submitters)

Cellular senescence consists of regulated phenotypes associated with permanent exit from the cell cycle in response to stressors such as genomic instability. The consequences of senescence go beyond individual cells due to the senescence associated secretory phenotype (SASP), which can induce inflammation in neighboring cells. Some cancers respond to CDK4/6 inhibitors (CDK4/6i) with a senescence-like phenotype in the absence of extensive DNA damage.

Read the full summary ↓

We asked how the SASP and the transcriptional regulatory profile triggered by CDK4/6i-driven arrest compares to the canonical NF-κB-regulated SASP triggered by DNA damage. We profiled the dynamics of transcriptional regulation in response to the CDK4/6i, palbociclib, and the DNA damaging agent, doxorubicin. We found upregulation of NF-κB driven-SASP genes was shared across both drugs, although delayed in CDK4/6i, coinciding with slower enhancer activation and epigenetic changes. ATM/ATR inhibition did not affect CDK4/6i-induced NF-κB nuclear localization, suggesting an alternative upstream activator. Inhibiting NF-κB suppressed the expression of SASP genes without reversing stable arrest, pointing to SASP manipulation as a potential therapeutic strategy and providing insights into controversies regarding cell cycle arrest-driven SASP.

Published in

CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation

Yeung JL, Rendleman J, Anderson Westcott L et al. · Life science alliance 2026 · PMID 42425764 · doi:10.26508/lsa.202603790

This dataset

Open GSE295260 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 GSE295260_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 PRJNA1253962 and SRA study SRP580394. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42425764) ↗

Study design

40 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 40 sample titles: 40 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

GSM8944501 LS8817, Cycling, rep1, RNA
GSM8944502 LS8817, Cycling, rep2, RNA
GSM8944503 LS8817, Cycling, rep3, RNA
GSM8944504 LS8817, day10, Doxo, rep1, RNA
GSM8944505 LS8817, day10, Palbo, rep1, RNA
GSM8944506 LS8817, day14, Doxo, rep1, RNA
GSM8944507 LS8817, day14, Doxo, rep2, RNA
GSM8944508 LS8817, day14, Palbo, rep1, RNA
GSM8944509 LS8817, day14, Palbo, rep2, RNA
GSM8944510 LS8817, day21, Doxo, rep1, RNA
GSM8944511 LS8817, day21, Doxo, rep2, RNA
GSM8944512 LS8817, day21, Palbo, rep1, RNA
GSM8944513 LS8817, day21, Palbo, rep2, RNA
GSM8944514 LS8817, day28, Palbo, rep1, RNA
GSM8944515 LS8817, day28, Palbo, rep2, RNA
GSM8944516 LS8817, day3, Doxo, rep1, RNA
GSM8944517 LS8817, day3, Doxo, rep2, RNA
GSM8944518 LS8817, day3, Palbo, rep1, RNA
GSM8944519 LS8817, day3, Palbo, rep2, RNA
GSM9844031 MCF7, PvsPFvsD, Cycling, rep1, RNA
GSM9844032 MCF7, PvsPFvsD, Cycling, rep2, RNA
GSM9844033 MCF7, PvsPFvsD, Cycling, rep3, RNA
GSM9844034 MCF7, PvsPFvsD, Cycling, rep4, RNA
GSM9844035 MCF7, day14Doxo, rep1, RNA
GSM9844036 MCF7, day14Doxo, rep2, RNA
GSM9844037 MCF7, day14Doxo, rep3, RNA
GSM9844038 MCF7, day21Palbo, rep1, RNA
GSM9844039 MCF7, day21Palbo, rep2, RNA
GSM9844040 MCF7, day21Palbo, rep3, RNA
GSM9844041 MCF7, day18PalboandFulv, rep1, RNA
GSM9844042 MCF7, day18PalboandFulv, rep2, RNA
GSM9844043 MCF7, Cycling, rep1, RNA
GSM9844044 MCF7, Cycling, rep2, RNA
GSM9844045 MCF7, Cycling, rep3, RNA
GSM9844046 MCF7, Day1, FulvPalbo, RNA
GSM9844047 MCF7, Day3, FulvPalbo, RNA
GSM9844048 MCF7, Day5, FulvPalbo, RNA
GSM9844049 MCF7, Day10, FulvPalbo, RNA
GSM9844050 MCF7, Day15, FulvPalbo, RNA
GSM9844051 MCF7, Day21, FulvPalbo, RNA

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