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Status |
Public on Apr 24, 2018 |
Title |
HI-C 2.0: AN OPTIMIZED HI-C PROCEDURE FOR HIGH-RESOLUTION GENOME-WIDE MAPPING OF CHROMOSOME CONFORMATION |
Organism |
Homo sapiens |
Experiment type |
Other
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Summary |
Chromosome conformation capture-based methods such as Hi-C have become mainstream techniques for the study of the 3D organization of genomes. These methods convert chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol for Hi-C (Hi-C 2.0) that integrates recent improvements into a single protocol for efficient and high-resolution capture of chromatin interactions. This protocol combines chromatin digestion and frequently cutting enzymes to obtain kilobase (Kb) resolution. It also includes steps to reduce random ligation and the generation of uninformative molecules, such as unligated ends, to improve the amount of valid intra-chromosomal read pairs. This protocol allows for obtaining information on conformational structures such as compartment and topologically associating domains, as well as high-resolution conformational features such as DNA loops.
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Overall design |
HI-C 2.0
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Contributor(s) |
Belaghzal H, Gibcus J, Dekker J |
Citation(s) |
28435001 |
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Submission date |
Apr 25, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
Job Dekker |
Organization name |
UMass Medical School
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Department |
Program in Systems Biology
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Lab |
Dekker Labaratory
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Street address |
368 Plantation Street
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City |
Worcester |
State/province |
Massachusetts |
ZIP/Postal code |
01605 |
Country |
USA |
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Platforms (1) |
GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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Samples (3) |
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Relations |
BioProject |
PRJNA384173 |
SRA |
SRP105181 |
Supplementary file |
Size |
Download |
File type/resource |
GSE98161_Geo_mappingStat.xlsx |
17.3 Kb |
(ftp)(http) |
XLSX |
GSE98161_RAW.tar |
6.2 Gb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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