GEO series
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
GSE6273
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
64 samples
Submitted 2007/01/01
Platform GPL4558Platform GPL4559Platform GPL1454
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 64 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
- 64 samples: 60 distinct titles, 1 of them repeatedGroups 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.
Summary (written by the submitters)
Eukaryotic gene regulatory information is contained within the DNA sequences of cis-regulatory elements and the epigenetic features of the chromatin surrounding these elements. Recent investigations in yeast, fly, and mammalian systems have made significant contributions toward our understanding of the relationship between gene activation and chromatin architecture at transcriptional promoters, but much work remains to improve our knowledge of this relationship at human promoters and other transcriptional regulatory elements, such as enhancers.
Read the full summary ↓
Here, we report that human promoters and enhancers are associated with distinct chromatin signatures that can be employed to predict these classes of regulatory elements in the human genome. Using a combination of chromatin immunoprecipitation (ChIP) and microarray (ChIP-chip) experiments, we generated high-resolution maps of the chromatin architecture along 30 Mbp of the human genome, located promoters and enhancers in these regions, and characterized the histone modification features of these regulatory elements. We found that active promoters are marked by tri-methylation of histone H3 lysine 4 (H3K4me3) at the transcriptional start site (TSS) and mono-methylation of this residue (H3K4me1) downstream and upstream of the TSS. In contrast, enhancers are marked by H3K4me1 but not H3K4me3. Both types of regulatory elements are also associated with nucleosome depletion and varying degrees of histone acetylation and H3K4me2. We developed computational prediction algorithms that employ the distinct chromatin signatures to identify new promoters and enhancers, predicting over 200 promoters and 400 enhancers within the 30 Mbp regions. This approach correctly predicted over 84% of the regulatory elements identified in an independent, unbiased study of transcription factor binding in the same regions. Our results suggest a histone code for distinct classes of transcriptional regulatory elements, offering insights into the functional relationships between chromatin modifications and regulatory activity in human cells and providing a new resource for the functional annotation of the human genome. Keywords: ChIP-chip
This dataset
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need.
3 · The original raw files
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE6273_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
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 PRJNA63415. Searching any of these in the dataset finder brings you back here.
Study design
60 distinct titles, 1 of them repeated
STAT1 HeLa RenLab ENCODE PCR tiling array ×5
How we read this: Read from 64 sample titles: 60 distinct titles with little repetition. 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
- GSM144303 STAT1 IFN-gamma ENCODE NimbleGen hg16 tiling array replicate 1/3
- GSM144304 STAT1 IFN-gamma ENCODE NimbleGen hg16 tiling array replicate 2/3
- GSM144305 STAT1 IFN-gamma ENCODE NimbleGen hg16 tiling array replicate 3/3
- GSM144306 H4ac unstimulated ENCODE NimbleGen hg17 tiling array.
- GSM144307 H3K4me2 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array.
- GSM144308 H3ac unstimulated ENCODE NimbleGen hg17 tiling array.
- GSM144310 H3K4me2 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144312 H3ac IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144313 H3K4me2 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144314 H3ac unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144315 H3K4me3 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144316 H3K4me3 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144317 H3K4me2 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144318 H3K4me2 unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144319 H3K4me3 unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144320 H3K4me2 unstimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144321 H3ac IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144322 H3K4me3 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144323 TAF1 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144324 H4ac unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144325 H4ac IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144326 RNAP unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144327 RNAP IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144328 RNAP unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144329 RNAP IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144330 H3ac unstimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144331 H3K4me3 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144332 H3K4me3 unstimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144333 RNAP IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144334 H3ac IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144335 H4ac unstimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144336 H4ac IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144337 H3K4me1 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144338 p300 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144339 H3 unstimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144340 H3K4me1 unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144341 H3K4me1 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 1.
- GSM144342 H3K4me1 IFN-gamma stimulated ENCODE NimbleGen hg17 tiling array replicate 2.
- GSM144343 H3K4me1 unstimulated ENCODE NimbleGen hg17 tiling array replicate 3.
- GSM144344 p300 unstimulated ENCODE NimbleGen hg17 tiling array replicate 2.
+ 24 more — browse all 64 samples with per-sample file links →
Datasets on a similar topic
- GSE126044 Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer 16 samples shares promoters, enhancers
- GSE298243 Single-Cell Profiling of DNA Methylation in Autism Spectrum Disorder Prefrontal Cortex Reveals Distinct Regulatory and Aging Signatures 49 samples shares signatures, distinct
- GSE315442 Transcriptomic profiling reveals distinct molecular signatures among lesion types in hidradenitis suppurativa 48 samples shares signatures, distinct
- GSE171817 SUMOylation Regulates Super-Enhancers Through Transcription Factor TFAP2C Binding on Chromatin 30 samples shares chromatin, enhancers
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares chromatin, distinct
- GSE314777 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer 10 samples shares chromatin, distinct
- GSE286581 Ablation of Linker Histone H1.4 Reveals Focal Regulation of AP-1 Directed Enhancers and Chromatin Accessibility [4sU] 6 samples shares chromatin, enhancers
- GSE142751 Genome-wide maps of chromatin state in 142 cancer cell lines [cell line] 855 samples shares chromatin
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.