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Series GSE128800 Query DataSets for GSE128800
Status Public on Jun 19, 2019
Title Comparing 3D genome organization in multiple species using Phylo-HMRF
Organisms Gorilla gorilla; Pan paniscus; Pan troglodytes
Experiment type Other
Summary We developed a continuous-trait probabilistic model to identify genome-wide evolutionary patterns of 3D genome structures based on multi-species Hi-C data. We applied the proposed method to analyzing cross-species Hi-C data from the same cell type in multiple primate species. The results showed that the proposed method enables discovery of distinct Hi-C contact frequency evolutionary patterns across species.
 
Overall design Comparing Hi-C contact frequencies among multiple primate species
 
Contributor(s) Yang Y, Zhang Y, Ren B, Dixon J, Ma J
Citation(s) 31229558
Submission date Mar 25, 2019
Last update date Jul 03, 2019
Contact name Yang Yang
E-mail(s) yy3@andrew.cmu.edu
Organization name Carnegie Mellon University
Department Computational Biology
Street address 5000 Forbes Ave
City Pittsburgh
State/province PA
ZIP/Postal code 15213
Country USA
 
Platforms (3)
GPL19148 Illumina HiSeq 2500 (Pan troglodytes)
GPL24148 Illumina HiSeq 2500 (Gorilla gorilla)
GPL24149 Illumina HiSeq 2500 (Pan paniscus)
Samples (3)
GSM3685694 Chimpanzee_Hi-C
GSM3685695 Bonobo_Hi-C
GSM3685696 Gorilla_Hi-C
Relations
BioProject PRJNA528916
SRA SRP189342

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
GSE128800_RAW.tar 5.1 Gb (http)(custom) TAR (of HIC, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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