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Series GSE169088 Query DataSets for GSE169088
Status Public on Apr 23, 2021
Title 3D genomics across the tree of life reveals condensin II as a determinant of architecture type
Organisms Arachis hypogaea; Triticum aestivum; Saccharomyces cerevisiae; Agaricus bisporus; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Drosophila melanogaster; Strongylocentrotus purpuratus; Ciona intestinalis; Branchiostoma lanceolatum; Xenopus laevis; Gallus gallus; Notamacropus eugenii; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Pleurobrachia bachei; Pygocentrus nattereri; Acropora millepora; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum; Python bivittatus; Hypsibius dujardini; Lethenteron camtschaticum
Experiment type Other
Summary We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
 
Overall design 26 species across the tree of life were included in the analysis, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.
 
Contributor(s) Dudchenko O, Lieberman Aiden E
Citation(s) 34045355
BioProject PRJNA512907
Submission date Mar 17, 2021
Last update date Jul 23, 2021
Contact name Olga Dudchenko
E-mail(s) Olga.Dudchenko@bcm.edu
Organization name Baylor College of Medicine
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (30)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
Samples (32)
GSM5182714 Tammar wallaby blood (Sample1096)
GSM5182715 Domestic chicken splenic-derived lymphocytes (Sample4077)
GSM5182716 Burmese python blood (Sample0838)
Relations
SRA SRP175152

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE169088_RAW.tar 26.8 Gb (http)(custom) TAR (of BEDPE, FASTA, HIC, VCF, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file
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