Weber Lab Workshop 1
Creators
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.
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
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