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Series GSE135910 Query DataSets for GSE135910
Status Public on May 21, 2020
Title Mapping PT modifications in bacteria
Organisms Salmonella enterica; Escherichia coli K-12
Experiment type Other
Summary One microbial organism always contains multiple DNA modification systems as defense strategies or epigenetic controls. Here, we describe crosstalk between two distinct DNA modifications with different target sequence motif: DNA phosphorothioation (PT, GPSAAC/GPSTTC by DndACDE proteins) and N6-methyl-adenine methylation (m6A, G6mATC by Dam protein). By using a newly developed DNA modification sequencing method PT nick-seq, we found that half of PT modifications change from GAAC/GTTC to GATC sites after bacteria have lost Dam.
 
Overall design Map the PT modification sites in bacteria and ∆dam mutant
To further confirm this result and get a full understanding of where the new modifications are, we exploited PT-nick-seq method to get the single-base resolution of PT modification map of E.coli BW25113 and ∆dam mutant harboring S. enterica DndBCDE proteins.With PT-nick-seq technology, PT modifications on DNA were turned into strand breaks after iodine cleavage and were inferred through the higher read coverage ratio compared to their neighbor nucleotides and negative controls.To further get the PT modification site information in the same ChIP-seq samples, PT-nick-seq was adopted to sequence the genomic DNA of the same strain used for ChIP-seq experiment.
 
Contributor(s) Wu X, Cao B, Wang L, Chen S, Dedon PC
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Submission date Aug 16, 2019
Last update date May 24, 2020
Contact name Xiaolin Wu
E-mail(s) xiaolinwu@whu.edu.cn
Organization name Singapore-MIT Alliance for Research and Technology (SMART)
Street address 1 CREATE Way
City Singapore
State/province Singapore
ZIP/Postal code 138602
Country Singapore
 
Platforms (2)
GPL27120 HiSeq X Ten (Escherichia coli K-12)
GPL27121 HiSeq X Ten (Salmonella enterica)
Samples (12)
GSM4037772 E.coli BW25113[pJTU1238]-iodine
GSM4037773 E.coli BW25113[pJTU1238]-ctrl
GSM4037774 E.coli BW25113[pJTU1980]-iodine
This SubSeries is part of SuperSeries:
GSE135949 Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria
Relations
BioProject PRJNA560558
SRA SRP218607

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
GSE135910_RAW.tar 582.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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