CDK4/6 Inhibition reprograms the Breast Cancer immunopeptidome via Rb-Dependent chromatin and transcriptomic remodeling
RNA-seq (gene expression) · human · 14 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
- 14 samples: 3 × MDA_Abema vs 3 × MDA_DMSO vs 3 × CAMA1_Abema vs 3 × CAMA1_DMSOGroups 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 reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodelingCell reports · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE287955_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1215355 and SRA study SRP559691. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 14 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.
- GSM8756247 MDA_Abema_1 MDA_Abema
- GSM8756248 MDA_Abema_2 MDA_Abema
- GSM8756249 MDA_Abema_3 MDA_Abema
- GSM8756250 MDA_DMSO_1 MDA_DMSO
- GSM8756251 MDA_DMSO_2 MDA_DMSO
- GSM8756252 MDA_DMSO_3 MDA_DMSO
- GSM8756253 CAMA1_Abema_1 CAMA1_Abema
- GSM8756254 CAMA1_Abema_2 CAMA1_Abema
- GSM8756255 CAMA1_Abema_3 CAMA1_Abema
- GSM8756256 CAMA1_DMSO_1 CAMA1_DMSO
- GSM8756257 CAMA1_DMSO_2 CAMA1_DMSO
- GSM8756258 CAMA1_DMSO_3 CAMA1_DMSO
- GSM8756259 MDAMB231_Abema
- GSM8756260 MDAMB231_DMSO
- GSE241598 Proteasome inhibition reprograms chromatin landscape in breast cancer (ChIP-Seq) 18 samples shares inhibition, reprograms, chromatin, breast
- GSE295260 CDK4/6 inhibition induces a senescence-associated secretory phenotype via delayed NF-κB activation 40 samples shares cdk4, inhibition
- GSE323965 Transcriptional signatures indicating RB function may predict response to CDK4/6 inhibition in endometrial cancer [RNA-Seq] 39 samples shares cdk4, inhibition
- GSE303100 Dissecting Resistance to CDK4/6 Inhibition in Experimental Glioma via Genome-wide CRISPR-Cas9 Screening 24 samples shares cdk4, inhibition
- GSE268699 Genes expression alterations associated with resistance to combined CDK4/6 inhibitor and endocrine therapy in ER+ breast cancer 18 samples shares cdk4, breast
- GSE330516 A non-canonical function of the tyrosine degradation enzyme FAH drives CDK4/6 inhibitor resistance in breast cancer I 16 samples shares cdk4, breast
- GSE298567 Single-Cell transcriptomics reveals biomarker heterogeneity linked to CDK4/6 Inhibitor resistance in breast cancer cell lines 14 samples shares cdk4, breast
- GSE325471 The CDK4/6 inhibitor dalpiciclib augments the antitumor efficacy of enzalutamide in preclinical models of castration-resistant prostate cancer through inhibition of MCM4-mediated DNA replication 12 samples shares cdk4, inhibition
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.