 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 09, 2009 |
| Title |
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.
The processed heatmap data, showing the number of read pairs corresponding to particular locus pairs in the genome, are linked to the Series record below.
The processed eigenvector data used to generate the heatmaps are linked to the Series record below.
Additional DNAseI and ChIP-Seq data tracks were used in the paper, and are available at the UCSC browser (http://genome.ucsc.edu/)
DNAseI:
wgEncodeUwDnaseSeqRawSignalRep2K562
wgEncodeUwDnaseSeqRawSignalRep2Gm06990
ChIP-Seq:
wgEncodeBroadChipSeqSignalGm12878H3k36me3
wgEncodeBroadChipSeqSignalGm12878H3k27me3
|
| |
|
| Overall design |
Interaction maps in 2 different cell types.
|
| |
|
| Contributor(s) |
Lieberman-Aiden E, Van Berkum N |
| Citation(s) |
19815776, 20461051 |
| Submission date |
Sep 21, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Erez Lieberman-Aiden |
| E-mail(s) |
erezl@princeton.edu
|
| Organization name |
Harvard/MIT/Broad
|
| Street address |
7 Cambridge Circle
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
|
| Samples (8)
|
| GSM455136 |
Hi-C (HindIII,GM,2) 3 |
| GSM455137 |
Hi-C (NcoI,GM,1) 1 |
| GSM455138 |
Hi-C (NcoI,GM,1) 2 |
| GSM455139 |
Hi-C (HindIII,K562,1) 7 |
| GSM455140 |
Hi-C (HindIII,K562,1) 8 |
|
| Relations |
| SRA |
SRP001261 |
| BioProject |
PRJNA119555 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE18199_3D-FISH.tar.gz |
2.3 Kb |
(ftp)(http) |
TAR |
| GSE18199_Globules.zip.gz |
231.3 Mb |
(ftp)(http) |
ZIP |
| GSE18199_Peano_curves.zip.gz |
283.0 Mb |
(ftp)(http) |
ZIP |
| GSE18199_RAW.tar |
1.1 Gb |
(http)(custom) |
TAR (of TXT) |
| GSE18199_binned_heatmaps.zip.gz |
1.0 Gb |
(ftp)(http) |
ZIP |
| GSE18199_eigenvector_files.zip.gz |
1.7 Mb |
(ftp)(http) |
ZIP |
| GSE18199_python_code.tar.gz |
30.2 Kb |
(ftp)(http) |
TAR |
| GSE18199_readme_v4.txt |
6.1 Kb |
(ftp)(http) |
TXT |
| GSE18199_supplemental_code.tar.gz |
7.2 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...