GEO series

Global Chromatin Modifications at Enhancers Correlate with Cell Type-Specific Gene Expression in the Human Genome

GSE14083 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 235 samples Submitted 2009/03/01 Platform GPL4173Platform GPL7874Platform GPL7831Platform GPL4167Platform GPL7857Platform GPL7811Platform GPL4170Platform GPL7851Platform GPL7814Platform GPL7854Platform GPL7808Platform GPL7834Platform GPL7865Platform GPL4138Platform GPL4164Platform GPL7848Platform GPL7842Platform GPL4161Platform GPL4141Platform GPL7845Platform GPL4144Platform GPL4165Platform GPL7846Platform GPL7809Platform GPL7866Platform GPL4168Platform GPL7849Platform GPL7806Platform GPL4142Platform GPL4162Platform GPL7820Platform GPL4156Platform GPL7837Platform GPL4139Platform GPL4179Platform GPL7840Platform GPL7860Platform GPL4176Platform GPL4159Platform GPL8072Platform GPL7843Platform GPL7863Platform GPL7880Platform GPL4153Platform GPL7817Platform GPL4137Platform GPL7864Platform GPL4140Platform GPL7867Platform GPL7861Platform GPL4157Platform GPL7841Platform GPL4177Platform GPL4160Platform GPL7844Platform GPL7838Platform GPL4163Platform GPL7881Platform GPL7818Platform GPL7812Platform GPL7855Platform GPL4174Platform GPL7815Platform GPL7858Platform GPL7852Platform GPL570Platform GPL7832Platform GPL7835Platform GPL4151Platform GPL4154Platform GPL4175Platform GPL7819Platform GPL4155Platform GPL4171Platform GPL7856Platform GPL7813Platform GPL4158Platform GPL7839Platform GPL7859Platform GPL4178Platform GPL7879Platform GPL4152Platform GPL7836Platform GPL4172Platform GPL4132Platform GPL7847Platform GPL7816Platform GPL7862Platform GPL7810Platform GPL7830Platform GPL4166Platform GPL7833Platform GPL4169Platform GPL7850Platform GPL7807Platform GPL4143Platform GPL7853

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 235 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: 235 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

The human body is composed of diverse cell types with distinct functions. While it is known that lineage specification depends on cell specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene1-3, the relative roles of these regulatory elements in this process is not clear.

Read the full summary ↓

We have previously developed a chromatin immunoprecipitation-based microarray method (ChIP-chip) to identify promoters, enhancers and insulator elements in the human genome4-6. Here, we use the same approach to identify these active elements in multiple cell types and investigated their roles in cell type-specific gene expression. We observed that chromatin state at promoters and CTCF-binding at insulators are largely invariant across diverse cell types. By contrast, enhancers are marked with highly cell type-specific histone modification patterns, strongly correlate to cell type-specific gene expression programs on a global scale, and are functionally active in a cell type-specific manner. Our results defined over 55, 000 potential transcriptional enhancers in the human genome, significantly expanding the current catalog of human enhancers and highlighting the role of these elements in cell type-specific gene expression. Keywords: ChIP-chip

This dataset

Open GSE14083 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

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 (GSE14083_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 PRJNA112507. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 19295514) ↗

Samples in this study

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+ 235 more — browse all 235 samples with per-sample file links →

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