GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE84502 Query DataSets for GSE84502
Status Public on Jul 18, 2017
Title Genome-wide maps of GlcNAc bound proteins and Pho ChIP-seq in Drosophila S2 cells and pupae.
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We developed a strategy to map GlcNAc modified proteins based on a chemical chromatin precipitation strategy. Drosophila S2 cells, as well as wild type (wt) and sxc null pupae, were fed with 100 uM Ac4GalNAz and the resulting DNA was cross-linked, sonicated, and purified. DNA strands cross-linked to GlcNAz proteins were isolated by congugating with alkyn-biotin by Staudinger ligation followed by streptavidin purification. The resulting DNA was constructed into libraries for sequencing. To asses the robustness of our strategy, we compared GalNAz ChIP-seq results in S2 cells with two other GlcNAc ChIP-seq strategies, using a mutant β-1,4-galactosyltransferase (GalT) and the lecting wheat germ agglutinin (WGA). Briefly, GalT was incubated with cross-linked, sonicated and purified DNA along with UDP-GalNAz. Ligation to biotin with click chemistry followed by streptavidin purification resulted in library ready material. For WGA and Pho ChIP-seq, cross-linked and purified DNA was incubated with pho antibody or WGA resin and purified followed by library preperation.
Overall design Examination GlcNAc bound loci in Drosophila cells and pupae.
Contributor(s) Liu T, Myschyshyn M, Sinclair D, Cecioni S, Beja K, Honda BM, Morin RD, Vocadlo D
Citation(s) 27918560
Submission date Jul 18, 2016
Last update date May 15, 2019
Contact name David Vocadlo
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 (1)
GPL16479 Illumina MiSeq (Drosophila melanogaster)
Samples (7)
GSM2238594 GlcNAc ChIP-seq on GalNAz fed S2 cells
GSM2238595 Pho ChIP-seq in S2 cells
GSM2238596 GlcNAc ChIP-seq on S2 cells using WGA purification
BioProject PRJNA329506
SRA SRP078807

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
GSE84502_RAW.tar 277.1 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap