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. Author manuscript; available in PMC: 2020 Mar 7.
Published in final edited form as: Cell. 2019 Feb 21;176(6):1502–1515.e10. doi: 10.1016/j.cell.2019.01.020
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Critical Commercial Assays
Deposited Data
HFF-hTERT dilution Hi-C This paper 4DN: 4DNES9L4AK6Q
HFF-hTERT clone 6 in-situ Hi-C 4D Nucleome 4DN: 4DNES2R6PUEK
Rao et al in-situ Hi-C Rao et al., 2013 GSE74072
Jin et al dilution Hi-C Jin et al., 2013 GSE85977
FISH spot positions and distances This paper 4DN: https://data.4dnucleome.org/publications/80007b23-7748-4492-9e49-c38400acbe60/
Experimental Models: Cell Lines
HFF-hTERT cells 4D Nucleome RRID: CVCL_VC40
Experimental Models: Organisms/Strains
Oligonucleotides
Recombinant DNA
BAC clones (See Table S1) CHORI See Table S1
Software and Algorithms
Bowtie2.2.8 Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Hiclib Imakaev et al., 2012 https://bitbucket.org/mirnylab/hiclib
Cooler Abdennur et al, 2017 http://doi.org/10.5281/zenodo.1039971
Lavaburst (domain calling algorithms) Schwarzer et al, 2017 https://github.com/nvictus/lavaburst
cWorld Lajoie et al., 2015 https://github.com/dekkerlab/cworld-dekker
Other