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| UID | Name | Scientist | Protocol | Parent | Treatment1 | Type | Species | Tissue | Morphology | Disease | Source | Catalog# | Link_Catalog# | Media | MediaSource |
| CEL-250422BAC-1 | HCT-116 | Vadim Backman | https://fairdomhub.org/sops/824 | clonocyte | Homo sapiens | Large intestine; Colon | epithelial | Carcinoma; Colorectal | ATCC | #CCL-247 | https://www.atcc.org/products/ccl-247 | McCoy’s 5A modified medium | Thermo Fisher Scientific #16600-082 | ||
| CEL-250422BAC-2 | U2OS | Vadim Backman | https://fairdomhub.org/sops/824 | Homo sapiens | Bone | epithelial | Osteosarcoma | ATCC | #HTB-96 | https://www.atcc.org/products/htb-96 | McCoy’s 5A modified medium | Thermo Fisher Scientific #16600-082 | |||
| CEL-250422BAC-3 | HeLa | Vadim Backman | https://fairdomhub.org/sops/824 | Homo sapiens | Uterus; Cervix | epithelial | Adenocarcinoma | ATCC | #CCL-2 | https://www.atcc.org/products/ccl-2 | RPMI 1640 | Thermo Fisher Scientific #11875127 | |||
| CEL-250422BAC-4 | BJ CRL-2522 | Vadim Backman | https://fairdomhub.org/sops/824 | fibroblast | Homo sapiens | Skin; Foreskin | fibroblast | N/A | ATCC | #CRL-2522 | https://www.atcc.org/products/crl-2522 | Minimum essential media | Thermo Fisher Scientific #11095080 | ||
| CEL-250422BAC-5 | A549 | Vadim Backman | https://fairdomhub.org/sops/824 | epithelial | Homo sapiens | Lung | epithelial | Carinoma | ATCC | #CCL-185 | https://www.atcc.org/products/ccl-185 | ||||
| CEL-250422BAC-6 | HCT-116 RAD21-mAID-Clover CMV-OsTIR1(F74G) | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-7 | BJ-ActD | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-4 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-8 | HCT-ActD | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-9 | HCT-GSK | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-10 | HCT-TSA | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-11 | HCT-BAPTA | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-12 | HeLa-ActD | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-3 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-13 | HeLa-GSK | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-3 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-14 | HeLa-TSA | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-3 | See Protocol for full treatment details | Homo sapiens | |||||||||
| CEL-250422BAC-15 | HCT-POLR1A | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | See reference 58 and 59 of the publication | ||||||||
| CEL-250422BAC-16 | HCT-POLR2A | Vadim Backman | https://fairdomhub.org/sops/824 | CEL-250422BAC-1 | See Protocol for full treatment details | Homo sapiens | See reference 58 and 59 of the publication | ||||||||
| CEL-250422BAC-17 | Myoblast | Vadim Backman | https://fairdomhub.org/sops/824 | human muscle | Homo sapiens | ||||||||||
| CEL-250422BAC-18 | Myotube | Vadim Backman | https://fairdomhub.org/sops/824 | human muscle | Homo sapiens | ||||||||||
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| UID | File_PrimaryData | Link_PrimaryData | Path_PrimaryData | Repository | RepositoryID | Scientist | Protocol | Parent | Instrument | Type | Targets | InstrumentType | ScanMode | Software |
| D.IMG-250422BAC-1 | A549.tif | https://datadryad.org/downloads/file_stream/3783746 | Figure_1.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-5 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | IMOD software and TomoPy penalized maximum likelihood algorithm | |
| D.IMG-250422BAC-2 | BJ.tif | https://datadryad.org/downloads/file_stream/3783746 | Figure_1.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-4 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | IMOD software and TomoPy penalized maximum likelihood algorithm | |
| D.IMG-250422BAC-3 | HCT116.tif | https://datadryad.org/downloads/file_stream/3783746 | Figure_1.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-1 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | IMOD software and TomoPy penalized maximum likelihood algorithm | |
| D.IMG-250422BAC-4 | A549 packing domain.jpg | https://datadryad.org/downloads/file_stream/3783746 | Figure_1.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-5 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | IMOD software and TomoPy penalized maximum likelihood algorithm | |
| D.IMG-250422BAC-5 | control rad21.nuc.tif | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/PWS Data/RAD21 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-1 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-6 | rad21 depleted.tif | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/PWS Data/RAD21 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-6 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-7 | ActD Control.tif | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/PWS Data/ActD | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-1 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-8 | ActD treated.tif | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/PWS Data/ActD | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-8 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-9 | actD_treated.jpg | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/ActD | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-7 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | ||
| D.IMG-250422BAC-10 | rad21_depleted.tif | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip/Rad21 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/825 | CEL-250422BAC-6 | Hitachi 2300 STEM | Chromatin Electron Microscopy | Scanning Transmission Electron Microscope (STEM) | High-angle annular dark-field (HAADF) | ||
| D.IMG-250422BAC-11 | SMLM_HeLa_DSMO | https://datadryad.org/downloads/file_stream/3783751 | Figure_5.zip/Figure 5/Figure 5 SMLM/dmso | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-3 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-12 | SMLM_HeLa_ActD | https://datadryad.org/downloads/file_stream/3783751 | Figure_5.zip/Figure 5/Figure 5 SMLM/act-d | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-12 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-13 | SMLM_HeLa_GSK | https://datadryad.org/downloads/file_stream/3783751 | Figure_5.zip/Figure 5/Figure 5 SMLM/gsk | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-13 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-14 | SMLM_HeLa_TSA | https://datadryad.org/downloads/file_stream/3783751 | Figure_5.zip/Figure 5/Figure 5 SMLM/tsa | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-14 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-15 | PWS bapta control.tif | https://datadryad.org/downloads/file_stream/3783750 | Figure 6.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-1 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-16 | PWS bapta treated.tif | https://datadryad.org/downloads/file_stream/3783750 | Figure 6.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/826 | CEL-250422BAC-11 | Hamamatsu C9100-13 EMCCD | Partial Wave Spectroscopic (PWS) Microscopy (Live-cell) | Leica DM IRB inverted microscope | Liquid Crystal Tunable Filter (LCTF, Cambridge Research & Instrumentation) | ||
| D.IMG-250422BAC-17 | HCT116_CTRL_Comp_50laser_30expt_cell2_ThunderStorm_thre2.tif | https://datadryad.org/downloads/file_stream/3783750 | Figure 6.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-1 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | |||
| D.IMG-250422BAC-18 | HCT116_BAPTA_Comp_50laser_30expt_cell4_ThunderSTORM_thre2.tif | https://datadryad.org/downloads/file_stream/3783750 | Figure 6.zip | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-11 | Single-molecule localization microscopy (SMLM) | H3K9me3, H3K27ac, RNA Polymerase II, H3K27me3 | Single-Molecule Localization Microscopy (SMLM) | |||
| D.IMG-250422BAC-19 | SMLM_HCT_DMSO | https://datadryad.org/downloads/file_stream/3783752 | Figure 7.zip/SMLM/dmso_EU_k9 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-1 | Single-molecule localization microscopy (SMLM) | EU, K9, Lamin, Nucleolus | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-20 | SMLM_HCT_GSK | https://datadryad.org/downloads/file_stream/3783752 | Figure 7.zip/SMLM/gsk_EU_k9 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-9 | Single-molecule localization microscopy (SMLM) | EU, K9, Lamin, Nucleolus | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
| D.IMG-250422BAC-21 | SMLM_HCT_TSA | https://datadryad.org/downloads/file_stream/3783752 | Figure 7.zip/SMLM/tsa_EU_k9 | Dryad | https://doi.org/10.5061/dryad.b8gtht7p0 | Vadim Backman | https://fairdomhub.org/sops/827 | CEL-250422BAC-10 | Single-molecule localization microscopy (SMLM) | EU, K9, Lamin, Nucleolus | Single-Molecule Localization Microscopy (SMLM) | ThunderSTORM plugin for ImageJ / FIJI | ||
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| UID | File_PrimaryData | Link_PrimaryData | Path_PrimaryData | Scientist | Protocol | Parent | SourceCode | SourceCode_Link | |
| A.IMG-250424BAC-1 | CVCvsR.xlsx | https://datadryad.org/downloads/file_stream/3783746 | Figure_1.zip | Vadim Backman | https://fairdomhub.org/sops/825 | D.IMG-250422BAC-1; D.IMG-250422BAC-2; D.IMG-250422BAC-3; D.IMG-250422BAC-4 | LogLog Domains.nb | https://datadryad.org/downloads/file_stream/3783746 | |
| A.IMG-250424BAC-2 | BJActD_Domains_2024.xlsx | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip | Vadim Backman | https://fairdomhub.org/sops/825 | D.IMG-250422BAC-9 | ActD Domain Lifecycle.nb | https://datadryad.org/downloads/file_stream/3783748 | |
| A.IMG-250424BAC-3 | control packing efficiency.xlsx | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip | Vadim Backman | https://fairdomhub.org/sops/825 | D.IMG-250422BAC-10 | RAD21 Domain Lifecycle.nb | https://datadryad.org/downloads/file_stream/3783748 | |
| A.IMG-250424BAC-4 | RAD21 packing efficiency.xlsx | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip | Vadim Backman | https://fairdomhub.org/sops/825 | D.IMG-250422BAC-10 | RAD21 Domain Lifecycle.nb | https://datadryad.org/downloads/file_stream/3783748 | |
| A.IMG-250424BAC-5 | Cody and Emily_Planetary Model_CD Edits.prism | https://datadryad.org/downloads/file_stream/3783748 | Figure_4.zip | Vadim Backman | https://fairdomhub.org/sops/826 | D.IMG-250422BAC-5; D.IMG-250422BAC-6; D.IMG-250422BAC-7; D.IMG-250422BAC-8 | |||
| A.IMG-250424BAC-6 | Ion Data for Paper.xlsx | https://datadryad.org/downloads/file_stream/3783750 | Figure 6.zip | Vadim Backman | https://fairdomhub.org/sops/827 | D.IMG-250422BAC-17; D.IMG-250422BAC-18 | |||
| A.IMG-250424BAC-7 | adq6652_movie_s1.mov | https://www.science.org/doi/suppl/10.1126/sciadv.adq6652/suppl_file/sciadv.adq6652_movies_s1_to_s4.zip | adq6652_movie_s1.mov | Vadim Backman | Movie S1. 3D ChromSTEM reconstruction of a control domain in A549 cells. Representative 3D tomogram of a packing domain in A549 cells. | D.IMG-250422BAC-1 | |||
| A.IMG-250424BAC-8 | adq6652_movie_s2.mov | https://www.science.org/doi/suppl/10.1126/sciadv.adq6652/suppl_file/sciadv.adq6652_movies_s1_to_s4.zip | adq6652_movie_s2.mov | Vadim Backman | Movie S2. 3D ChromSTEM reconstruction of a domain in ActD treated BJ cells. Representative 3D tomogram of a packing domain demonstrating increased spreading and decreased efficiency of packing. | D.IMG-250422BAC-2 | |||
| A.IMG-250424BAC-9 | adq6652_movie_s3.mov | https://www.science.org/doi/suppl/10.1126/sciadv.adq6652/suppl_file/sciadv.adq6652_movies_s1_to_s4.zip | adq6652_movie_s3.mov | Vadim Backman | Movie S3. 3D ChromSTEM reconstruction of a domain in RAD21 depleted HCT-116 cells. Representative 3D tomogram of a mature packing domain in RAD21 depleted cells demonstrating intact structure. | D.IMG-250422BAC-3 | |||
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| UID | Name | Protocol | Scientist | Parent | DNA Type | ||||
| DNA-250422BAC-1 | HCT-POLR1A_Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-15 | Illumina Library | ||||
| DNA-250422BAC-2 | HCT-POLR1A_Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-15 | Illumina Library | ||||
| DNA-250422BAC-3 | HCT-POLR2A_Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-16 | Illumina Library | ||||
| DNA-250422BAC-4 | HCT-POLR2A_Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-16 | Illumina Library | ||||
| DNA-250422BAC-5 | HCT-116_Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-1 | Illumina Library | ||||
| DNA-250422BAC-6 | HCT-116_Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-1 | Illumina Library | ||||
| DNA-250422BAC-7 | HCT-ActD_Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-8 | Illumina Library | ||||
| DNA-250422BAC-8 | HCT-ActD_Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-8 | Illumina Library | ||||
| DNA-250422BAC-9 | Myoblast Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-17 | Illumina Library | ||||
| DNA-250422BAC-10 | Myoblast Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-17 | Illumina Library | ||||
| DNA-250422BAC-11 | Myotube Rep1 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-18 | Illumina Library | ||||
| DNA-250422BAC-12 | Myotube Rep2 | https://fairdomhub.org/sops/828 | Vadim Backman | CEL-250422BAC-18 | Illumina Library | ||||
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| UID | File_PrimaryData | Link_PrimaryData | Scientist | Protocol | Type | Description | AdditionalData | AdditionalData_Link | |
| MDL-250424BAC-1 | Figure 2.zip | https://datadryad.org/downloads/file_stream/3783747 | Vadim Backman | https://fairdomhub.org/sops/829 | AlphaFold Modeling | AlphaFold PDB directory has structural models of chromatin enzymes obtained from alphafold. Calculate Rg Enzymes.py is a python script that generates Enzyme sites.xlsx, and SR-EV Domain Penetration Results.nb models enzyme penetration into chromatin domains as a function of size (Rg) using a physical simulation (SR-EV = Stochastic Returning Excluded Volume model) | Movie S4: In silico polymer-based chromatin model showing compaction (CN 0–12) | https://www.science.org/doi/suppl/10.1126/sciadv.adq6652/suppl_file/sciadv.adq6652_movies_s1_to_s4.zip | |
| MDL-250424BAC-2 | Figure 3.zip | https://datadryad.org/downloads/file_stream/3783745 | Vadim Backman | https://fairdomhub.org/sops/829 | Domain Loop Modeling | Version1.5_ps0.1 Contains simulation outputs modeling the evolution of chromatin packing domains over time (3hr, 8hr, 100hr), which is then associated with PM_Figures_Vfinal.ipynb, a jupyter notebook that connects to the phenomelogical loop domain formation model | |||
