DOI: 10.5281/zenodo.8040563
title: Weber Lab Workshop 1

description: This data will be used to used to illustrate diversity in contact probability curves P(s) from HiC data across a variety of organisms. All data is publicly available and comes from the following references: From: Hoencamp, C., Dudchenko, O., Elbatsh, A. M., Brahmachari, S., Raaijmakers, J. A., van Schaik, T., ... & Rowland, B. D. (2021). 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science, 372(6545), 984-989.<br> GSM5182714 Tammar wallaby blood (Sample1096)<br> GSM5182715 Domestic chicken splenic-derived lymphocytes (Sample4077)<br> GSM5182716 Burmese python blood (Sample0838)<br> GSM5182717 African clawed frog fibroblast (XTC) (Sample4078)<br> GSM5182718 Red-bellied piranha muscle (Sample2033)<br> GSM5182719 Brownbanded bamboo shark blood (Sample1575)<br> GSM5182720 Arctic lamprey muscle (Sample3820)<br> GSM5182721 Sea squirt tissue (Sample2441, Sample2444)<br> GSM5182722 Sea squirt tissue (Sample2441)<br> GSM5182723 European lancelet whole animal(s) (Sample1824)<br> GSM5182724 Purple sea urchin muscle (Sample2581)<br> GSM5182725 Yellow fever mosquito whole animal(s) (SAMN08028733, SAMN08028734, SAMN08028735)<br> GSM5182726 Yellow fever mosquito whole animal(s) (SAMN08028734)<br> GSM5182727 Southern house mosquito whole animal(s) (SAMN06546149)<br> GSM5182728 Fruit fly whole animal(s) (Sample4079)<br> GSM5182729 Tardigrade whole animal(s) (Sample3840)<br> GSM5182730 Roundworm whole animal(s) (Sample4082)<br> GSM5182731 Chinese liver fluke whole animal(s) (Sample2741)<br> GSM5182732 California sea hare mix of CNS cells (Sample1819)<br> GSM5182733 Moss animal whole animal(s) (Sample1845)<br> GSM5182734 Acropora millepora stony coral branch fragments (Sample1884, Sample1992)<br> GSM5182735 Sea gooseberry tissue (Sample1830)<br> GSM5182736 Common mushroom fruiting body (Sample3828)<br> GSM5182737 Baker's yeast cells (Sample4076)<br> GSM5182738 Peanut leaves (Sample2455)<br> GSM5182739 Bread wheat leaves (Sample4080, Sample4081)<br> GSM5182740 Chinese muntjac blood (Sample1296)<br> GSM5182741 Chinese muntjac fibroblasts (Sample2606)<br> GSM5182742 Indian muntjac (Sample2604, Sample3923)<br> GSM5182743 Indian muntjac fibroblasts (Sample3923)<br> GSM5182744 Fruit fly PnM cell line (SAMN10242997) From: Rao, S. S., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., ... & Aiden, E. L. (2014). A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell, 159(7), 1665-1680.<br> 4DNFIJTOIGOI.mcool Human IMR90 cells, see: https://data.4dnucleome.org/files-processed/4DNFIJTOIGOI/ From Schloissnig, S., Kawaguchi, A., Nowoshilow, S., Falcon, F., Otsuki, L., Tardivo, P., ... & Tanaka, E. M. (2021). The giant axolotl genome uncovers the evolution, scaling, and transcriptional control of complex gene loci. Proceedings of the National Academy of Sciences, 118(15), e2017176118.<br> Al1.zoom.mcool Axolotl Al1 cells From: Marinov, G. K., Trevino, A. E., Xiang, T., Kundaje, A., Grossman, A. R., & Greenleaf, W. J. (2021). Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. Nature Genetics, 53(5), 613-617.<br> GSM4658994 Dinoflagellate Breviolum minutum From: Nand, A., Zhan, Y., Salazar, O. R., Aranda, M., Voolstra, C. R., & Dekker, J. (2021). Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum. Nature Genetics, 53(5), 618-629.<br> GSE152150 Dinoflagellate Symbiodinium microadriaticum coccoid Smic 1.1N <br>