GEO series

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

GSE8854 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2008/05/07 Platform GPL5666Platform GPL5646Platform GPL5729Platform GPL5649Platform GPL5669Platform GPL5667Platform GPL5644Platform GPL5668Platform GPL5648

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: 10 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Proper genome functionality is underpinned by the non-random, spatial or ganisation of chromatin. At the periphery of the nucleus, the association of chr omatin with the nuclear lamina is thought to facilitate both structural organisa tion and regulation of gene expression. Except for a small number of individual loci, the regions of the human genome that locate at the nuclear lamina have not been identified.

Read the full summary ↓

Here we used DamID to map the interaction sites of lamin B1 at high resolution in human fibroblasts. We show that almost half of the human gen ome preferentially associates with the nuclear lamina. Chromatin-lamina interact ions occur via sharply demarcated domains of up to several megabases in size, wh ich are bordered by similar sized domains that do not associate with the lamina. Lamina associated domains (LADs) are typified by low gene density and low gene expression levels. This is reflected by low levels of PolII binding and histone modification H3K4me2, in combination with enrichment of H3K27me3 (and H3K9?). A considerable subset of LADs is flanked by active promoters pointing outwards, or by the insulator protein CTCF, suggesting possible mechanisms of LAD confinemen t. Finally, we found that chromosome re-arrangements occur more frequently betwe en loci located either within or outside LADs. The identification of enormous, s harply defined stretches of the human genome that associate with the nuclear lam ina provides unprecedented insights into the 3D organisation of chromatin within the nucleus. Our results reveal the division of the human genome into periphera l and internal domains, which is echoed in genome functionality. Keywords: DamID

This dataset

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE8854_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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 PRJNA102207. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 18463634) ↗

Samples in this study

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+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE277500 Coordinated control of genome-nuclear lamina interactions by Topoisomerase 2B and Lamin B receptor (pA-DamID) 226 samples shares interactions, nuclear, lamina
GSE289252 Lamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity 46 samples shares organization, nuclear
GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares revealed, lamina
GSE295224 Dual single-cell and bulk RNA sequencing reveal transcriptional profiles underlying heterogenous host-parasite interactions in human peripheral blood mononuclear cells 42 samples shares interactions, nuclear
GSE317257 Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Respons 35 samples shares interactions, mapping
GSE300197 The cytoskeleton drives abnormal chromatin-lamina interactions in LMNA-deficient cardiomyocytes. 30 samples shares interactions, lamina
GSE293428 Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response [scRNA-Seq] 18 samples shares interactions, mapping
GSE279180 Cell type mapping reveals tissue niches and interactions in subcortical multiple sclerosis lesions [snRNA-seq] 16 samples shares interactions, mapping

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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