Genome-wide Chromatin Interaction Mapping

4C was performed as described (24 (link),25 (link)). Proximity ligation junctions, reflecting in vivo spatial proximity, were generated with DpnII (New England Biolabs), followed by circularization with Csp6I (Thermo Scientific). Chromosomal contacts with the TSS-containing fragment were amplified with inverse PCR primers (Supplementary Table S1), and sequenced on the Illumina 2000 platform.

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Portuguez A.S., Grbesa I., Tal M., Deitch R., Raz D., Kliker L., Weismann R., Schwartz M., Loza O., Cohen L., Marchenkov-Flam L., Sung M.H., Kaplan T, & Hakim O. (2022). Ep300 sequestration to functionally distinct glucocorticoid receptor binding loci underlie rapid gene activation and repression. Nucleic Acids Research, 50(12), 6702-6714.

Publication 2022

DpnII Csp6I

Chromosomal Inverse pcr Ligation Primers

Corresponding Organization : Bar-Ilan University

Other organizations : National Institutes of Health, Hebrew University of Jerusalem

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Variable analysis

independent variables

Performing 4C protocol as described (references 24 and 25)

dependent variables

Chromosomal contacts with the TSS-containing fragment

control variables

Use of DpnII (New England Biolabs) for proximity ligation junctions
Use of Csp6I (Thermo Scientific) for circularization
Use of inverse PCR primers (Supplementary Table S1) for amplification
Sequencing on the Illumina 2000 platform

controls

No positive or negative controls were explicitly mentioned.

Annotations

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