GEO series

Lamin B1 depletion in senescent cells triggers large-Scale changes in gene expression and in the chromatin landscape[ChIP-seq]

GSE36616 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 17 samples Submitted 2013/09/09 Platform GPL10999Platform GPL11154

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 17 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: 17 samples: 4 × Proliferating H3K27me3 ChIP vs 2 × Proliferating Histone 3 ChIP vs 2 × Senescent Histone 3 ChIP vs 2 × Senescent H3K27me3 ChIPGroups 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)

Cellular senescence is a stable proliferation arrest in response to stress, associated with an altered secretory pathway (Senescence Associated Secretory Phenotype (SASP)). Senescence-associated proliferation arrest and the SASP are thought to act in concert to promote tumor suppression and tissue aging. While chromatin regulation and down regulation of lamin B1 have been implicated as effectors of cell senescence, functional interactions between them are poorly understood.

Read the full summary ↓

We compared the genome-wide distributions of H3K4me3 and H3K27me3 between proliferating and senescent primary human cells and found dramatic differences, including large-scale domains of H3K4me3- and H3K27me3-enriched "mesas" and H3K27me3-depleted "canyons" in senescent cells. Senescent mesas form at the sites of lamin B1-associated domains (LADs) in proliferating cells. Mesas also overlap with regions that exhibit DNA hypomethylation in cancer, suggesting that chromatin changes in pre-malignant senescent cells foreshadow epigenetic changes in cancer. Proliferating fibroblasts from Hutchinson-Gilford Progeria Syndrome patients expressing mutant lamin A (progerin) also show evidence of H3K4me3 mesas, suggesting a link between premature chromatin changes and accelerated cell senescence and tissue aging. In contrast, canyons form mostly in between LADs and are enriched in genes, gene promoters and enhancers. Strikingly, H3K27me3 loss in canyons is correlated with upregulation of key senescence genes, including genes comprising the SASP, indicating a link between global changes in chromatin structure and local regulation of gene expression. Finally, premature reduction of lamin B1 in midlife proliferating cells triggers formation of senescence-associated mesas and canyons and accelerated senescence. Together, our data illustrate a profound reorganization of chromatin during senescence, and suggest that down regulation of lamin B1 in senescence is a key trigger of global and local chromatin changes that impact gene expression, aging and cancer.

This dataset

Open GSE36616 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE36616_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 PRJNA155425 and SRA study SRP011584. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 23934658) ↗

Study design

4 × Proliferating H3K27me3 ChIP vs 2 × Proliferating Histone 3 ChIP vs 2 × Senescent Histone 3 ChIP vs 2 × Senescent H3K27me3 ChIP

Supports a case/control comparison: 2 samples read as cases, 2 as controls.

How we read this: 4 replicated groups read from 17 sample titles; they account for 10 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

GSM897555 Proliferating Histone 3 ChIP Proliferating Histone 3…
GSM897556 Proliferating H3K4me3 ChIP
GSM897557 Proliferating H3K27me3 ChIP R1 Proliferating H3K27me3 …
GSM897558 Proliferating LaminB1 ChIP
GSM897559 Senescent Histone 3 ChIP Senescent Histone 3 ChIP
GSM897560 Senescent H3K4me3 ChIP
GSM897561 Senescent H3K27me3 ChIP R1 Senescent H3K27me3 ChIP
GSM1135038 Proliferating Histone 3 ChIP R2 Proliferating Histone 3…
GSM1135039 Senescent Histone 3 ChIP R2 Senescent Histone 3 ChIP
GSM1135040 Proliferating H3K27me3 ChIP R2 Proliferating H3K27me3 …
GSM1135041 Proliferating H3K27me3 ChIP R3 Proliferating H3K27me3 …
GSM1135042 Proliferating H3K27me3 ChIP R4 Proliferating H3K27me3 …
GSM1135043 Senescent H3K27me3 ChIP R2 Senescent H3K27me3 ChIP
GSM1135044 Control H3
GSM1135045 OIS Ras-Induced H3
GSM1135046 Control H3K4me3
GSM1135047 OIS Ras-Induced H3K4me3

Datasets on a similar topic

GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares chromatin, chip-seq
GSE282760 Epigenomic manipulation reveals the relationship between locus specific chromatin dynamics and gene expression [ChIP-seq] 36 samples shares chromatin, chip-seq
GSE337829 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq] 32 samples shares chromatin, chip-seq
GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares chromatin, chip-seq
GSE303855 Mechanistic and Epigenetic Partitioning of Lamina-Associated Chromatin Revealed by a Genome-Wide Imaging Screen 45 samples shares chromatin, lamin
GSE300197 The cytoskeleton drives abnormal chromatin-lamina interactions in LMNA-deficient cardiomyocytes. 30 samples shares chromatin, lamin
GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
GSE327821 Single-molecule, single-cell profiling of linked chromatin states [Single_cell_CoCUT&Tag] 200 samples shares chromatin

Search all human ChIP / ATAC / CUT&Tag 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.