← BioTransfer GEO Dataset Finder
GEO series

Transcriptional properties of LIG1-heterozygous-knockout (hetKO) vs. LIG1-WT cells in MCF-12A TP53-null and TP53-WT cells

GSE329371 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2026/05/25 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: 8 conditions, mostly in duplicateGroups 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)
Proteogenomic analyses has identified an association between LIG1 (DNA Ligase I) loss and chemotherapy resistance in a subset of triple negative breast cancer (TNBC) enriched for TP53 mutation. Here, we demonstrated that co-occurrence of TP53 mutations and LIG1 loss is associated with upregulated DDR activity, including homologous recombination, likely contributing to reduced platinum sensitivity.
Read the full summary ↓
Unbiased genetic and monotherapy drug screens identified PARP inhibitiors (PARPi) as a potential treatment for LIG1-depleted tumors, however the increase in sensitivity was modest and lower than levels observed in TNBC models with homologous recombination deficiency. Subsequently, a screen of PARP inhibition in combination with each of 120 clinically relevant DDR inhibitors revealed that PARPi sensitivity in LIG1-loss cells was significantly enhanced by addition of ATR inhibitior (ATRi). Olaparib and ceralasertib demonstrated synergistic cytotoxicity in LIG1-loss cell line models; the combination significantly reduced tumor volume in LIG1-low PDX model compared to either monotherapy, and showed greater ex vivo cytotoxicity in LIG1-low PDX organoids versus LIG1-high control. Hence, this study highlights LIG1-status as a stratification factor into ongoing and future clinical trials of DDR-targeted combinations in TNBCs.
This dataset
Open GSE329371 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 GSE329371_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 PRJNA1458741 and SRA study SRP695669. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
8 conditions, mostly in duplicate
MCF-12A TP53-WT LIG1-WT EP ×2 MCF-12A TP53-WT LIG1-WT LP ×2 MCF-12A TP53-WT LIG1-hetKO1 EP ×2 MCF-12A TP53-WT LIG1-hetKO1 LP ×2 MCF-12A TP53-null LIG1-WT EP ×2 MCF-12A TP53-null LIG1-WT LP ×2 MCF-12A TP53-null LIG1-hetKO1 EP ×2 MCF-12A TP53-null LIG1-hetKO1 LP ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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 →

Share this dataset

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.