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| Datafile metadata | How to use this sheet Details on how to use this sheet and what the cells mean can be found by visiting: | ||||||||
| Data File Title: | samples-publish_VB-CC_MDL.xlsx | ||||||||
| Data File Description: | Batch sample publishing | ||||||||
| Project SEEK ID: | https://fairdomhub.org/projects/340 | ||||||||
| Master metadata sheet guide | |||||||||
| Associated Assay | |||||||||
| Existing Assay SEEK ID: | https://fairdomhub.org/assays/2641 | ||||||||
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| New Assay metadata | |||||||||
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| Assay type: | Experimental_assay_type | Powered by: | |||||||
| Technology type: | Technology_type | ||||||||
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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 | |||
