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Effect of CMA inhibitor on gene expression in A549 non-small cell lung cancer cells

GSE291058 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/05/04 Platform GPL34284
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
Lung cancerThis series is part of our curated briefing on it.
Samples
12 samples: 3 × A549 cells, RARa WT + DMSO vs 3 × A549 cells, RARa WT + CIM7 vs 3 × A549 cells, RARa AHT + DMSO vs 3 × A549 cells, RARa AHT + CIM7Groups 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
Small molecule disruption of RARα/NCoR1 interaction inhibits chaperone-mediated autophagy in cancerEMBO molecular medicine · 2025
Summary (written by the submitters)
Transcriptomics of A549 cells treated with CIM7 in the presence of WT or AHT RARa to evaluate gene expression changes.
Published in
Small molecule disruption of RARα/NCoR1 interaction inhibits chaperone-mediated autophagy in cancer
McCabe M, Bhattacharyya R, Sereda R et al. · EMBO molecular medicine 2025 · PMID 40490560 · doi:10.1038/s44321-025-00254-y
This dataset
Open GSE291058 in finder → Find more human RNA-seq datasets → Lung 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 GSE291058_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 PRJNA1231472 and SRA study SRP567900. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40490560) ↗
Study design
3 × A549 cells, RARa WT + DMSO vs 3 × A549 cells, RARa WT + CIM7 vs 3 × A549 cells, RARa AHT + DMSO vs 3 × A549 cells, RARa AHT + CIM7

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 Lung cancer datasets

Search all human RNA-seq datasets in GEO →

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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.