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Series GSE18199 Query DataSets for GSE18199
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 Feb 21, 2019
Contact name Erez Lieberman-Aiden
E-mail 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)
GSM455133 Hi-C (HindIII,GM,1)
GSM455134 Hi-C (HindIII,GM,Biological Repeat)
GSM455135 Hi-C (HindIII,GM,2) 2
Relations
SRA SRP001261
BioProject PRJNA119555

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
Processed data provided as supplementary file
Raw data are available in SRA
Processed data is available on Series record

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