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Transcriptome changes in MCF7 cells after treatment with NONO ligands and controls

GSE299099 Homo sapiens (human) RNA-seq (gene expression) 30 samples Submitted 2025/06/09 Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 30 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
30 samples: 10 conditions, mostly in triplicateGroups 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
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONOCell chemical biology · 2026
Summary (written by the submitters)
RNA-Sequencing to determine transcriptome changes in MCF7 cells after treatment with NONO ligands and controls. NONO knockout (sgNONO) or control (sgControl) cells were treated.
Published in
Structural and mechanistic analysis of covalent ligands targeting the RNA-binding protein NONO
Lindsey GL, Hockley TK, Gomez AV et al. · Cell chemical biology 2026 · PMID 41534524 · doi:10.1016/j.chembiol.2025.12.010
This dataset
Open GSE299099 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 GSE299099_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 PRJNA1272574 and SRA study SRP590540. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41534524) ↗
Study design
10 conditions, mostly in triplicate
Total_RNAseq_MCF7_sgControl_6hours_R,R-GL-373 ×3 Total_RNAseq_MCF7_sgControl_6hours_S,S-GL-373 ×3 Total_RNAseq_MCF7_sgControl_6hours_DMSO ×3 Total_RNAseq_MCF7_sgControl_6hours_R-SKBG-1 ×3 Total_RNAseq_MCF7_sgControl_6hours_S-SKBG-1 ×3 Total_RNAseq_MCF7_sgNONO_6hours_R,R-GL-373 ×3 Total_RNAseq_MCF7_sgNONO_6hours_S,S-GL-373 ×3 Total_RNAseq_MCF7_sgNONO_6hours_DMSO ×3 +2 more

Supports a between-group comparison across 30 samples.

How we read this: 10 replicated groups read from 30 sample titles; they account for 30 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
Datasets on a similar topic

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