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RNA-seq gene expression profile of SUM159PT breast cancer cell line upon manipulation of two TDMD triggers, NREP and SERPINE1

GSE236783 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2026/06/30 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 5 × SUM159PT_SERPINE1_MRE_KO_clone vs 4 × SUM159PT_CRISPRi_NREP_KD_sgRNA vs 3 × SUM159PT_wild_type_unedited_clone vs 3 × SUM159PT_CRISPRi_CTRL_sgRNAGroups 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)
We investigate the effect of the perturbation of two transcripts involved in target-dependent microRNA degradation (TDMD): NREP is a trigger for miR-29b; SERPINE1 is a trigger for miR-30. We perturbed the genes and monitored the activity of miR-29 or miR-30 analysing the expression changes of their predicted target genes by RNA sequencing.
This dataset
Open GSE236783 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 GSE236783_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 PRJNA992422 and SRA study SRP447928. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 × SUM159PT_SERPINE1_MRE_KO_clone vs 4 × SUM159PT_CRISPRi_NREP_KD_sgRNA vs 3 × SUM159PT_wild_type_unedited_clone vs 3 × SUM159PT_CRISPRi_CTRL_sgRNA

Supports a between-group comparison across 15 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 15 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

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.