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Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (pA-DamID)

GSE277500 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 226 samples Submitted 2025/09/15 Platform GPL24676Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 226 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
226 samples: 83 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.
Paper
Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptorNucleic acids research · 2025
Summary (written by the submitters)
Lamina-associated domains (LADs) are megabase-sized genomic regions anchored to the nuclear lamina (NL). Factors controlling the interactions of the genome with the NL have largely remained elusive. Here, we identified DNA topoisomerase 2 beta (TOP2B) as a regulator of these interactions. TOP2B binds predominantly to inter-LAD (iLAD) chromatin and its depletion results in a partial loss of genomic partitioning between LADs and iLADs, suggesting that this enzyme might protect specific iLADs from interacting with the NL.
Read the full summary ↓
TOP2B depletion affects LAD interactions with lamin B receptor (LBR) more than with lamins. LBR depletion phenocopies the effects of TOP2B depletion, despite the different positioning of the two proteins in the genome. This suggests a complementary mechanism for organising the genome at the NL. Indeed, co-depletion of TOP2B and LBR causes partial LAD/iLAD inversion, reflecting changes typical of oncogene-induced senescence. We propose that a coordinated axis controlled by TOP2B in iLADs and LBR in LADs maintains the partitioning of the genome between the NL and the nuclear interior.
Published in
Coordinated control of genome-nuclear lamina interactions by topoisomerase 2B and lamin B receptor
van Schaik T, Magnitov M, de Haas M et al. · Nucleic acids research 2025 · PMID 41002030 · doi:10.1093/nar/gkaf964
This dataset
Open GSE277500 in finder → Find more human 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 GSE277500_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1162536 and SRA study SRP533422. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41002030) ↗
Study design
83 conditions, mostly in duplicate
pA-DamID_RPE1_SunTag_SCII_DAM ×5 pA-DamID_RPE1_SunTag_SCII_LB2 ×5 pA-DamID_RPE1_SunTag_TOP2BKD_DAM ×4 pA-DamID_RPE1_SunTag_TOP2BKD_LB2 ×4 pA-DamID_RPE1_iCUT_WT_SCII_DAM ×4 pA-DamID_RPE1_iCUT_WT_SCII_LB2 ×4 pA-DamID_RPE1_iCUT_WT_TOP2BKD_DAM ×4 pA-DamID_RPE1_iCUT_WT_TOP2BKD_LB2 ×4 +90 more

Supports a between-group comparison across 211 samples.

How we read this: 83 replicated groups read from 226 sample titles; they account for 211 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

+ 186 more — browse all 226 samples with per-sample file links →

Datasets on a similar topic

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