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Series GSE124785 Query DataSets for GSE124785
Status Public on Jan 07, 2020
Title A chemical genetic method for monitoring genome-wide dynamics of O-GlcNAc turnover on chromatin-associated proteins.
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary O-linked N-acetylglucosamine (O-GlcNAc) is a necessary protein modification installed onto hundreds of nucleocytoplasmic proteins by O-GlcNAc transferase (OGT). Recently, we developed an antibody-free metabolic feeding approach that enables unbiased mapping of O-GlcNAcylated proteins in a genome-wide manner, providing insight into the regulation of genes by O-GlcNAcylated proteins within Drosophila. Here we apply this O-GlcNAc chemical mapping strategy to a time course (TC) feeding experiment within Drosophila larvae, generated the first ever TC ChIP-seq experiment performed on both a protein modification and within a living organism. TC metabolic labeling experiments were performed in wild-type and O-GlcNAc hydrolase (OGA) deficient Drosophila. Analysis of the resulting sequencing data revealed that a loss of OGA causes a global increase in the retention of O-GlcNAc modification on proteins bound to the genome, suggesting most nuclear proteins are sensitive to effects of O-GlcNAc cycling. Interestingly, some loci are more sensitive to the impacts of a loss of OGA compared to others. This study will present an improved understanding of the regulation of gene expression by O-GlcNAc while providing the broader community with experimental methods for time-resolved analysis of genome-wide binding by proteins.
 
Overall design Time course O-GlcNAc-seq and OGA ChIP-seq in wild type (WT) and OGA knockout (OGA-null) Drosophila larvae.
 
Contributor(s) Liu T, Myschyshyn M, Sinclair D, Vocadlo D
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Submission date Jan 08, 2019
Last update date Jan 09, 2020
Contact name David Vocadlo
E-mail(s) [email protected]
Organization name Simon Fraser University
Department Chemistry
Street address 8888 University Drive
City Burnaby
State/province British Columbia
ZIP/Postal code V5A 1S6
Country Canada
 
Platforms (2)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
GPL19132 Illumina NextSeq 500 (Drosophila melanogaster)
Samples (38)
GSM3554032 O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 0h growth on DMSO media
GSM3554033 O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 4h growth on DMSO media
GSM3554034 O-GlcNAcseq_wt Drosophila larvae (biological rep 1)_150uM GalNAz media for 36h followed by 8h growth on DMSO media
Relations
BioProject PRJNA513484
SRA SRP176629

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE124785_OGA-ChIP-seq-peaks.bed.gz 25.5 Kb (ftp)(http) BED
GSE124785_RAW.tar 2.8 Gb (http)(custom) TAR (of BEDGRAPH)
GSE124785_TC-O-GlcNAc-seq-peaks.bed.gz 166.0 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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