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Series GSE160490 Query DataSets for GSE160490
Status Public on Jun 03, 2021
Title Hi-C Analyses with GENOVA: a case study with cohesin variants
Organism Homo sapiens
Experiment type Other
Summary Conformation capture-approaches like Hi-C can elucidate chromosome structure at a genome-wide scale. Hi-C datasets are large and require specialised software. Here, we present GENOVA: a user-friendly software package to analyse and visualise conformation capture data. GENOVA is an R-package that includes the most common Hi-C analyses, such as compartment and insulation score analysis. It can create annotated heatmaps to visualise the contact frequency at a specific locus and aggregate Hi-C signal over a user-specified genomic regions such as ChIP-seq data. Finally, our package supports output from the major mapping-pipelines. We demonstrate the capabilities of GENOVA by analysing Hi-C data from HAP1 cell lines in which the cohesin-subunits SA1 and SA2 were knocked out. We find that ΔSA1 cells gain intra-TAD interactions and increase compartmentalisation. ΔSA2 cells have longer loops and a less compartmentalised genome. These results suggest that cohesinSA1 forms longer loops, while cohesinSA2 plays a role in forming and maintaining intra-TAD interactions. The differences in loop-forming activity affect whole chromosome organisation consistent with a model where loops and compartments counterbalance each other. We show that GENOVA is an easy to use R-package, that allows researchers to explore Hi-C data in great detail.
 
Overall design Hi-C; Hap1 SA1 and SA2 knock-out cells
 
Contributor(s) van der Weide RH, de Wit E
Citation(s) 34046591
Submission date Oct 30, 2020
Last update date Jun 03, 2021
Contact name Robin H. van der Weide
Organization name Hubrecht Institute
Lab Kind Lab
Street address Uppsalalaan 8
City Utrecht
State/province Utrecht
ZIP/Postal code 3584 CT
Country Netherlands
 
Platforms (1)
GPL20795 HiSeq X Ten (Homo sapiens)
Samples (4)
GSM4873986 SA1 Hi-C rep 1
GSM4873987 SA2 Hi-C rep 1
GSM4873988 SA1 Hi-C rep 2
Relations
BioProject PRJNA673398
SRA SRP290149

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
GSE160490_RAW.tar 12.4 Gb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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