Weber Lab Workshop 1

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.
GSM5182714    Tammar wallaby blood (Sample1096)
GSM5182715    Domestic chicken splenic-derived lymphocytes (Sample4077)
GSM5182716    Burmese python blood (Sample0838)
GSM5182717    African clawed frog fibroblast (XTC) (Sample4078)
GSM5182718    Red-bellied piranha muscle (Sample2033)
GSM5182719    Brownbanded bamboo shark blood (Sample1575)
GSM5182720    Arctic lamprey muscle (Sample3820)
GSM5182721    Sea squirt tissue (Sample2441, Sample2444)
GSM5182722    Sea squirt tissue (Sample2441)
GSM5182723    European lancelet whole animal(s) (Sample1824)
GSM5182724    Purple sea urchin muscle (Sample2581)
GSM5182725    Yellow fever mosquito whole animal(s) (SAMN08028733, SAMN08028734, SAMN08028735)
GSM5182726    Yellow fever mosquito whole animal(s) (SAMN08028734)
GSM5182727    Southern house mosquito whole animal(s) (SAMN06546149)
GSM5182728    Fruit fly whole animal(s) (Sample4079)
GSM5182729    Tardigrade whole animal(s) (Sample3840)
GSM5182730    Roundworm whole animal(s) (Sample4082)
GSM5182731    Chinese liver fluke whole animal(s) (Sample2741)
GSM5182732    California sea hare mix of CNS cells (Sample1819)
GSM5182733    Moss animal whole animal(s) (Sample1845)
GSM5182734    Acropora millepora stony coral branch fragments (Sample1884, Sample1992)
GSM5182735    Sea gooseberry tissue (Sample1830)
GSM5182736    Common mushroom fruiting body (Sample3828)
GSM5182737    Baker's yeast cells (Sample4076)
GSM5182738    Peanut leaves (Sample2455)
GSM5182739    Bread wheat leaves (Sample4080, Sample4081)
GSM5182740    Chinese muntjac blood (Sample1296)
GSM5182741    Chinese muntjac fibroblasts (Sample2606)
GSM5182742    Indian muntjac (Sample2604, Sample3923)
GSM5182743    Indian muntjac fibroblasts (Sample3923)
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.
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.
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.
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.
GSE152150    Dinoflagellate Symbiodinium microadriaticum coccoid Smic 1.1N