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Series GSE63525 Query DataSets for GSE63525
Status Public on Dec 11, 2014
Title A three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary 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, which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs ‘facing’ one another. The inactive X-chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
Overall design in situ Hi-C and dilution Hi-C were used to probe the three-dimensional structure of the genome in eight diverse human cell types and one mouse cell type.

Detailed information about all files (and file formats) uploaded to GEO for this study can be found in the supplementary file 'GSE63525_OVERALL_README.rtf'.
Contributor(s) Rao S, Huntley M, Lieberman Aiden E
Citation(s) 25497547, 26499245
Submission date Nov 20, 2014
Last update date May 15, 2019
Contact name Suhas Rao
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Lab The Center for Genome Architecture
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (5)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (200)
GSM1551550 HIC001
GSM1551551 HIC002
GSM1551552 HIC003
BioProject PRJNA268125
SRA SRP050102

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
GSE63525_CH12-LX_Arrowhead_domainlist.txt.gz 75.9 Kb (ftp)(http) TXT
GSE63525_CH12-LX_HiCCUPS_looplist.txt.gz 167.3 Kb (ftp)(http) TXT
GSE63525_CH12-LX_HiCCUPS_looplist_with_motifs.txt.gz 231.0 Kb (ftp)(http) TXT
GSE63525_CH12-LX_README.rtf 8.8 Kb (ftp)(http) RTF
GSE63525_CH12-LX_combined.hic 8.6 Gb (ftp)(http) HIC
GSE63525_CH12-LX_combined_30.hic 6.0 Gb (ftp)(http) HIC
GSE63525_CH12-LX_interchromosomal_contact_matrices.tar.gz 4.9 Gb (ftp)(http) TAR
GSE63525_CH12-LX_intrachromosomal_contact_matrices.tar.gz 1.8 Gb (ftp)(http) TAR
GSE63525_CH12_combined_30.hic 163.8 Mb (ftp)(http) HIC
GSE63525_GM12878_HiCCUPS_chrX_superloop_list.txt.gz 2.0 Kb (ftp)(http) TXT
GSE63525_GM12878_SNPs.txt.gz 7.4 Mb (ftp)(http) TXT
GSE63525_GM12878_combined_README.rtf 13.4 Kb (ftp)(http) RTF
GSE63525_GM12878_combined_interchromosomal_contact_matrices.tar.gz 35.0 Gb (ftp)(http) TAR
GSE63525_GM12878_combined_intrachromosomal_contact_matrices.tar.gz 23.2 Gb (ftp)(http) TAR
GSE63525_GM12878_dilution_combined.hic 10.9 Gb (ftp)(http) HIC
GSE63525_GM12878_dilution_combined_30.hic 7.8 Gb (ftp)(http) HIC
GSE63525_GM12878_diploid_intrachromosomal_contact_matrices.tar.gz 1.5 Gb (ftp)(http) TAR
GSE63525_GM12878_diploid_maternal.hic 1.3 Gb (ftp)(http) HIC
GSE63525_GM12878_diploid_paternal.hic 1.3 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_DpnII_combined.hic 6.8 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_DpnII_combined_30.hic 4.4 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_noXlink_combined.hic 5.5 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_noXlink_combined_30.hic 4.4 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_primary+replicate_combined.hic 51.0 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_primary+replicate_combined_30.hic 37.2 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_primary.hic 31.9 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_primary_30.hic 23.5 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_replicate.hic 29.1 Gb (ftp)(http) HIC
GSE63525_GM12878_insitu_replicate_30.hic 21.1 Gb (ftp)(http) HIC
GSE63525_GM12878_primary+replicate_Arrowhead_domainlist.txt.gz 242.3 Kb (ftp)(http) TXT
GSE63525_GM12878_primary+replicate_HiCCUPS_looplist.txt.gz 658.8 Kb (ftp)(http) TXT
GSE63525_GM12878_primary+replicate_HiCCUPS_looplist_with_motifs.txt.gz 827.1 Kb (ftp)(http) TXT
GSE63525_GM12878_primary_HiCCUPS_looplist.txt.gz 420.0 Kb (ftp)(http) TXT
GSE63525_GM12878_primary_README.rtf 9.0 Kb (ftp)(http) RTF
GSE63525_GM12878_primary_interchromosomal_contact_matrices.tar.gz 14.6 Gb (ftp)(http) TAR
GSE63525_GM12878_primary_intrachromosomal_contact_matrices.tar.gz 7.1 Gb (ftp)(http) TAR
GSE63525_GM12878_replicate_HiCCUPS_looplist.txt.gz 372.5 Kb (ftp)(http) TXT
GSE63525_GM12878_replicate_README.rtf 8.9 Kb (ftp)(http) RTF
GSE63525_GM12878_replicate_interchromosomal_contact_matrices.tar.gz 13.5 Gb (ftp)(http) TAR
GSE63525_GM12878_replicate_intrachromosomal_contact_matrices.tar.gz 6.5 Gb (ftp)(http) TAR
GSE63525_GM12878_subcompartments.bed.gz 31.1 Kb (ftp)(http) BED
GSE63525_HMEC_Arrowhead_domainlist.txt.gz 104.0 Kb (ftp)(http) TXT
GSE63525_HMEC_HiCCUPS_looplist.txt.gz 304.9 Kb (ftp)(http) TXT
GSE63525_HMEC_HiCCUPS_looplist_with_motifs.txt.gz 405.0 Kb (ftp)(http) TXT
GSE63525_HMEC_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_HMEC_combined.hic 7.1 Gb (ftp)(http) HIC
GSE63525_HMEC_combined_30.hic 5.0 Gb (ftp)(http) HIC
GSE63525_HMEC_interchromosomal_contact_matrices.tar.gz 3.8 Gb (ftp)(http) TAR
GSE63525_HMEC_intrachromosomal_contact_matrices.tar.gz 1.7 Gb (ftp)(http) TAR
GSE63525_HUVEC_Arrowhead_domainlist.txt.gz 107.7 Kb (ftp)(http) TXT
GSE63525_HUVEC_HiCCUPS_looplist.txt.gz 203.5 Kb (ftp)(http) TXT
GSE63525_HUVEC_HiCCUPS_looplist_with_motifs.txt.gz 279.3 Kb (ftp)(http) TXT
GSE63525_HUVEC_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_HUVEC_combined.hic 8.9 Gb (ftp)(http) HIC
GSE63525_HUVEC_combined_30.hic 6.8 Gb (ftp)(http) HIC
GSE63525_HUVEC_interchromosomal_contact_matrices.tar.gz 4.8 Gb (ftp)(http) TAR
GSE63525_HUVEC_intrachromosomal_contact_matrices.tar.gz 2.4 Gb (ftp)(http) TAR
GSE63525_HeLa_Arrowhead_domainlist.txt.gz 114.2 Kb (ftp)(http) TXT
GSE63525_HeLa_HiCCUPS_looplist.txt.gz 163.6 Kb (ftp)(http) TXT
GSE63525_HeLa_HiCCUPS_looplist_with_motifs.txt.gz 219.0 Kb (ftp)(http) TXT
GSE63525_IMR90_Arrowhead_domainlist.txt.gz 195.3 Kb (ftp)(http) TXT
GSE63525_IMR90_HiCCUPS_looplist.txt.gz 513.8 Kb (ftp)(http) TXT
GSE63525_IMR90_HiCCUPS_looplist_with_motifs.txt.gz 657.7 Kb (ftp)(http) TXT
GSE63525_IMR90_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_IMR90_combined.hic 12.8 Gb (ftp)(http) HIC
GSE63525_IMR90_combined_30.hic 8.9 Gb (ftp)(http) HIC
GSE63525_IMR90_interchromosomal_contact_matrices.tar.gz 5.9 Gb (ftp)(http) TAR
GSE63525_IMR90_intrachromosomal_contact_matrices.tar.gz 3.8 Gb (ftp)(http) TAR
GSE63525_K562_Arrowhead_domainlist.txt.gz 151.9 Kb (ftp)(http) TXT
GSE63525_K562_HiCCUPS_looplist.txt.gz 362.6 Kb (ftp)(http) TXT
GSE63525_K562_HiCCUPS_looplist_with_motifs.txt.gz 472.9 Kb (ftp)(http) TXT
GSE63525_K562_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_K562_combined.hic 12.1 Gb (ftp)(http) HIC
GSE63525_K562_combined_30.hic 9.1 Gb (ftp)(http) HIC
GSE63525_K562_interchromosomal_contact_matrices.tar.gz 6.4 Gb (ftp)(http) TAR
GSE63525_K562_intrachromosomal_contact_matrices.tar.gz 3.3 Gb (ftp)(http) TAR
GSE63525_KBM7_Arrowhead_domainlist.txt.gz 126.7 Kb (ftp)(http) TXT
GSE63525_KBM7_HiCCUPS_looplist.txt.gz 141.9 Kb (ftp)(http) TXT
GSE63525_KBM7_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_KBM7_combined.hic 13.9 Gb (ftp)(http) HIC
GSE63525_KBM7_combined_30.hic 10.2 Gb (ftp)(http) HIC
GSE63525_KBM7_interchromosomal_contact_matrices.tar.gz 8.5 Gb (ftp)(http) TAR
GSE63525_KBM7_intrachromosomal_contact_matrices.tar.gz 2.9 Gb (ftp)(http) TAR
GSE63525_NHEK_Arrowhead_domainlist.txt.gz 152.9 Kb (ftp)(http) TXT
GSE63525_NHEK_HiCCUPS_looplist.txt.gz 234.3 Kb (ftp)(http) TXT
GSE63525_NHEK_HiCCUPS_looplist_with_motifs.txt.gz 319.0 Kb (ftp)(http) TXT
GSE63525_NHEK_README.rtf 8.7 Kb (ftp)(http) RTF
GSE63525_NHEK_combined.hic 11.3 Gb (ftp)(http) HIC
GSE63525_NHEK_combined_30.hic 8.1 Gb (ftp)(http) HIC
GSE63525_NHEK_interchromosomal_contact_matrices.tar.gz 6.8 Gb (ftp)(http) TAR
GSE63525_NHEK_intrachromosomal_contact_matrices.tar.gz 2.3 Gb (ftp)(http) TAR
GSE63525_OVERALL_README.rtf 98.1 Kb (ftp)(http) RTF
GSE63525_RAW.tar 1.0 Tb (http)(custom) TAR (of HIC, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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