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Series GSE98161 Query DataSets for GSE98161
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
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.
 
Overall design HI-C 2.0
 
Contributor(s) Belaghzal H, Gibcus J, Dekker J
Citation(s) 28435001
Submission date Apr 25, 2017
Last update date Jul 25, 2021
Contact name Job Dekker
Organization name UMass Medical School
Department Program in Systems Biology
Lab Dekker Labaratory
Street address 368 Plantation Street
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (3)
GSM2588815 K562_R1
GSM2588816 K562_R2
GSM2588817 K562_R3
Relations
BioProject PRJNA384173
SRA SRP105181

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
GSE98161_Geo_mappingStat.xlsx 17.3 Kb (ftp)(http) XLSX
GSE98161_RAW.tar 6.2 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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