GSE125656
Exonuclease combinations reduce noises in 3D genomics technologies
Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased valid-pairs ratio from 30-40% to 70-80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency. Overall design: For dilution system, LIC-Hi-C treatments mean the noises of Hi-C were removed by “Lambda and Exonuclease I” exonuclease combination for 1h, which has three replicates (LIC-Hi-C-1,LIC-Hi-C-2,LIC-Hi-C-3). LRC-Hi-C-1, which means the noises of Hi-C were removed by “Lambda and RecJF” exonuclease combination for 1h.LRC-Hi-C 2-4(three replicates), which means the noises of Hi-C were removed by “Lambda and RecJF” exonuclease combination for 1 min. The formers are belong to Exo-Hi-C. Hi-C 1-3 (three replicates) are Exo-Hi-C control without exonuclease combination treatment. GSM862721(Standard Hi-C 1),GSM1718027(Standard Hi-C 2) and GSM862720(Standard Hi-C 3) are also set as control groups.We have downloaded these three data.We re-analyzed and named them as Standard Hi-C 1, Standard Hi-C 2 and Standard Hi-C 3 in our papers. For in situ system, IIIIC-in situ Hi-C 4-6 (three replicates) and 10-12 (another three replicates) treatments mean in situ Hi-C in this study were treated by  “Exonuclease I and Exonuclease III” exonuclease combination for 1 min. LIC-in situ Hi-C 4-6 (three replicates) and 10-11 (another two replicates)  treatments mean in situ Hi-C in this study were treated by  “Lambda and Exonuclease I” exonuclease combination for 1 min. The formers are belong to In situ exo-Hi-C.In situ Hi-C 1-3 (three replicates) and 12-14 (another three replicates) are in situ exo-Hi-C control without exonuclease combination treatment (named as in situ Hi-C). HIC088,HIC094,HIC096 are also set as control groups.We have downloaded these three data.We re-analyzed and named them as Rao et al. insitu Hi-C in our papers.