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GenomicsComprehensive mapping of long-range interactions reveals folding principles of the human genome.
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 chromosom...
ORGANISM(S): Homo sapiens 
2009-10-09 | E-GEOD-18199 | biostudies-arrayexpress
UnknownThe expanding scope of DNA sequencing.
Not available
S-EPMC4149750 | biostudies-literature
TranscriptomicsTranscription profiling of human lymphoblastoid cell line GM06690 in conjunction with Hi-C to determine the three-dimensional architecture of the genome
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 chromosom...
ORGANISM(S): Homo sapiens 
2009-10-10 | E-GEOD-18350 | biostudies-arrayexpress
TranscriptomicsA three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping
We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1-kilobase resolution. We find that genomes are partitioned into local domains, w...
ORGANISM(S): Homo sapiens 
2014-12-11 | E-GEOD-63525 | biostudies-arrayexpress
UnknownCTCF loss has limited effects on global genome architecture in Drosophila despite critical regulatory functions.
Not available
S-EPMC7880997 | biostudies-literature
TranscriptomicsDeletion of DXZ4 on the human inactive X chromosome eliminates superdomains and impairs gene silencing
During interphase, the inactive X chromosome (Xi) adopts an unusual 3D configuration known as the Barr body and is largely transcriptionally silent. Despite the importance of X inactivation, little is known about the 3D configuration of Xi and its relationship to gene silencing. We recently showed t...
ORGANISM(S): Homo sapiens 
2016-07-19 | E-GEOD-71831 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of mouse ES cells, neural precursor cells and embryonic fibroblasts
Expression profiles for isogenic (129SvJae x C57BL/6) murine embryonic stem (ES) cells, neural precursors (NPC) obtained through in vitro differentiation of the ES cells, and embryonic fibroblasts (MEF) obtained at day 13.5. Experiment Overall Design: 3 replicates of wt ES cells, 3 replicates of wt...
ORGANISM(S): Mus musculus 
2008-06-15 | E-GEOD-8024 | biostudies-arrayexpress
Unknown3D genomics across the tree of life reveals condensin II as a determinant of architecture type.
Not available
S-EPMC8172041 | biostudies-literature
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