GEO series

High Mobility Group Box protein 3 (HMGB3) facilitates DNA interstrand crosslink processing and double-strand break repair in human cells

GSE285696 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2025/06/01 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)
Samples: 16 samples: 4 × Wild Type U2OS cells, vs 4 × HMGB3 Knock-out U2OS cells, Clone 2, vs 4 × HMGB3 Knock-out U2OS cells, Clone 5, vs 4 × HMGB3 Knock-out U2OS cells, Clone 6,Groups 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: High-Mobility Group Box Protein 3 (HMGB3) Facilitates DNA Interstrand Crosslink Processing and Double-Strand Break Repair in Human CellsGenes · 2025

Summary (written by the submitters)

DNA damaging agents can contribute to genetic instability, and such agents are often used in cancer chemotherapeutic regimens due to their cytotoxicity. Thus, understanding the mechanisms involved in DNA damage processing can not only enhance our knowledge of basic DNA repair mechanisms, but may also be used to develop improved chemotherapeutic strategies to treat cancer.

Read the full summary ↓

The high mobility group box protein 1 (HMGB1) is a known nucleotide excision repair (NER) co-factor, and its family member HMGB3 has been implicated in chemo-resistance in ovarian cancer. Here, we aim to understand the potential role(s) of HMGB3 in processing DNA damage. A potential role in NER was investigated using HMGB3 knockout human cell lines in response to UV damage. Interestingly, unlike HMGB1, HMGB3 does not appear to play a role in NER. Subsequently, potential roles in DNA interstrand crosslink (ICL) and DNA double-strand break (DSB) repair were investigated using mutagenesis assays, metaphase spreads, foci formation, a variety of DNA repair assays, and Tag-Seq analyses in human cells. We found evidence to suggest that HMGB3 is involved in the processing of both DSBs and ICLs in human cells. These novel results elucidate a role for HMGB3 in DNA damage repair, and surprisingly, also indicate a distinct role of HMGB3 in DNA damage repair from that of HMGB1. These findings advance our understanding of the role of HMGB3 in chemotherapeutic drug resistance and as a target for new chemotherapeutic strategies in the treatment of cancer.

Published in

High-Mobility Group Box Protein 3 (HMGB3) Facilitates DNA Interstrand Crosslink Processing and Double-Strand Break Repair in Human Cells

Dangerfield J, Mukherjee A, Reh W et al. · Genes 2025 · PMID 41009989 · doi:10.3390/genes16091044

This dataset

Open GSE285696 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 GSE285696_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 PRJNA1205666 and SRA study SRP554905. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41009989) ↗

Study design

4 × Wild Type U2OS cells, vs 4 × HMGB3 Knock-out U2OS cells, Clone 2, vs 4 × HMGB3 Knock-out U2OS cells, Clone 5, vs 4 × HMGB3 Knock-out U2OS cells, Clone 6,

Supports a between-group comparison across 16 samples.

How we read this: 4 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

GSM8706883 Wild Type U2OS cells, replicate 1 Wild Type U2OS cells,
GSM8706884 Wild Type U2OS cells, replicate 2 Wild Type U2OS cells,
GSM8706885 Wild Type U2OS cells, replicate 3 Wild Type U2OS cells,
GSM8706886 Wild Type U2OS cells, replicate 4 Wild Type U2OS cells,
GSM8706887 HMGB3 Knock-out U2OS cells, Clone 2, replicate 1 HMGB3 Knock-out U2OS ce…
GSM8706888 HMGB3 Knock-out U2OS cells, Clone 2, replicate 2 HMGB3 Knock-out U2OS ce…
GSM8706889 HMGB3 Knock-out U2OS cells, Clone 2, replicate 3 HMGB3 Knock-out U2OS ce…
GSM8706890 HMGB3 Knock-out U2OS cells, Clone 2, replicate 4 HMGB3 Knock-out U2OS ce…
GSM8706891 HMGB3 Knock-out U2OS cells, Clone 5, replicate 1 HMGB3 Knock-out U2OS ce…
GSM8706892 HMGB3 Knock-out U2OS cells, Clone 5, replicate 2 HMGB3 Knock-out U2OS ce…
GSM8706893 HMGB3 Knock-out U2OS cells, Clone 5, replicate 3 HMGB3 Knock-out U2OS ce…
GSM8706894 HMGB3 Knock-out U2OS cells, Clone 5, replicate 4 HMGB3 Knock-out U2OS ce…
GSM8706895 HMGB3 Knock-out U2OS cells, Clone 6, replicate 1 HMGB3 Knock-out U2OS ce…
GSM8706896 HMGB3 Knock-out U2OS cells, Clone 6, replicate 2 HMGB3 Knock-out U2OS ce…
GSM8706897 HMGB3 Knock-out U2OS cells, Clone 6, replicate 3 HMGB3 Knock-out U2OS ce…
GSM8706898 HMGB3 Knock-out U2OS cells, Clone 6, replicate 4 HMGB3 Knock-out U2OS ce…

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