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Series GSE153950 Query DataSets for GSE153950
Status Public on Jul 08, 2020
Title Transcription-dependent domain-scale 3D genome organization in dinoflagellates
Organism Breviolum minutum
Experiment type Other
Summary Dinoflagellate chromosomes represent a unique evolutionary experiment, as they exist in a permanently condensed, liquid crystalline state, are not packaged by histones, and contain genes organized into polycistronic arrays, with minimal transcriptional regulation. We analyze the 3D genome of {Breviolum minutum}, and find large topological domains without chromatin loops, demarcated by convergent gene array boundaries (``dinoTADs’’). Transcriptional inhibition degrades dinoTADs, implicating transcription-induced supercoiling as the primary topological force in dinoflagellates.
 
Overall design Hi-C libraries associated with the project
 
Contributor(s) Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ
Citation(s) 33927397
Submission date Jul 07, 2020
Last update date Jun 03, 2021
Contact name Georgi Kolev Marinov
Organization name STANFORD UNIVERSITY
Department Genetics
Street address 279 Campus Drive West, Beckman Center, B-257A/259
City Stanford
State/province California
ZIP/Postal code 94305-5101
Country USA
 
Platforms (1)
GPL28838 Illumina NextSeq 500 (Breviolum minutum)
Samples (35)
GSM4658994 L142-Symbiodinium_minutum_SSb01-HIC
GSM4658995 L533-Symbiodinium_27C_Hi-C
GSM4658996 L534-Symbiodinium_34C_Hi-C
Relations
BioProject PRJNA644604
SRA SRP270673

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

Supplementary file Size Download File type/resource
GSE153950_RAW.tar 36.0 Gb (http)(custom) TAR (of HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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