GEO series

NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [Affymetrix]

GSE53999 Homo sapiens (human) Expression microarray 12 samples Submitted 2014/09/29 Platform GPL16043

At a glance

Expression microarray · human · 12 samples

What it is: Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism: Homo sapiens (human)
Samples: 12 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

Proinflammatory stimuli rapidly and globally remodel chromatin landscape, thereby enabling transcriptional responses. Yet, the mechanisms coupling chromatin regulators to the master regulatory inflammatory transcription factor NF-kB remain poorly understood. We report in human endothelial cells (ECs) that activated NF-kB binds to enhancers, provoking a rapid, global redistribution of BRD4 preferentially at super-enhancers, large enhancer domains highly bound by chromatin regulators.

Read the full summary ↓

Newly established NF-kB super-enhancers drive nearby canonical inflammatory response genes. In both ECs and macrophages BET bromodomain inhibition prevents super-enhancer formation downstream of NF-kB activation, abrogating proinflammatory transcription. In TNFa-activated endothelium this culminates in functional suppression of leukocyte rolling, adhesion and transmigration. Sustained BET bromodomain inhibitor treatment of LDLr -/- animals suppresses atherogenesis, a disease process rooted in pathological vascular inflammation involving endothelium and macrophages. These data establish BET-bromodomains as key effectors of inflammatory response through their role in the dynamic, global reorganization of super-enhancers during NF-kB activation.

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 (GSE53999_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: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA234306. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25263595) ↗

Samples in this study

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+ 12 more — browse all 12 samples with per-sample file links →

Datasets on a similar topic

GSE54000 NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers 36 samples shares proinflammatory, super-enhancers, brd4-dependent, coordinates, remodeling, nf-kb, rapid
GSE53998 NF-kB coordinates rapid, BRD4-dependent remodeling of proinflammatory super-enhancers [ChIP-Seq] 21 samples shares proinflammatory, super-enhancers, brd4-dependent, coordinates, remodeling, nf-kb, rapid
GSE292717 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [RNA-Seq] 42 samples shares super-enhancers, remodeling
GSE292716 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [ChIP-seq] 20 samples shares super-enhancers, remodeling
GSE44929 Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers [Affymetrix] 18 samples shares super-enhancers, affymetrix
GSE292718 Super-enhancers-driven SOX4/SMAD3 enhances AXL signaling via membrane phospholipid remodeling to accelerate leukemia progression [CUT&Tag] 16 samples shares super-enhancers, remodeling
GSE112713 Normothermic machine perfusion (NMP) inhibits proinflammatory responses in the liver and promotes regeneration 48 samples shares proinflammatory
GSE40386 SChLAP-1, a long non-coding RNA, antagonizes the SWI/SNF complex and coordinates aggressive prostate cancer. 28 samples shares coordinates

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