NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE138204 Query DataSets for GSE138204
Status Public on Mar 29, 2021
Title Pseudomonas syringae Virulence Regulatory Network construction
Organism Pseudomonas savastanoi pv. phaseolicola 1448A
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Pseudomonas syringae, a Gram-negative plant pathogen, infects more than 50 crops with its type III secretion system (T3SS) and causes severe economic losses around the world. Although the mechanisms of virulence-associated regulators of P. syringae T3SS have been studied for decades, the crosstalk and network underlying these regulators are still elusive. Previously, we have individually studied a group of T3SS regulators, including AefR, HrpS, and RhpRS. In the present study, we found 4 new T3SS regulator genes (envZ, ompR, tsiS and phoQ) via transposon-mediated mutagenesis. Two-component systems EnvZ and TsiS natively regulate T3SS. In order to uncover the crosstalk between 16 virulence-associated regulators, (including AefR, AlgU, CvsR, GacA, HrpL, HrpR, HrpS, MgrA, OmpR, PhoP, PilR, PsrA, RhpR, RpoN, TsiR and Vfr) in P. syringae, we mapped an intricate network named PSVnet (Pseudomonas syringae Virulence Regulatory Network) by combining differentially expression genes in RNA-seq and binding loci in ChIP-seq of all regulators.
 
Overall design ChIP-seq and RNA-seq for PSVnet
 
Contributor(s) Deng X
Citation(s) 33789108
Submission date Sep 30, 2019
Last update date Jun 28, 2021
Contact name Xin DENG
E-mail(s) [email protected]
Phone 852-34425693
Organization name City University of Hong Kong
Department Department of Biomedical Sciences
Lab Dr Xin DENG's Lab
Street address 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong
City Hong Kong
ZIP/Postal code 000000
Country Hong Kong
 
Platforms (1)
GPL24018 Illumina HiSeq 2000 (Pseudomonas savastanoi pv. phaseolicola 1448A)
Samples (148)
GSM4101911 PhoP-1-ChIP
GSM4101912 PhoP-2-ChIP
GSM4101913 MgrA-1-ChIP
Relations
BioProject PRJNA575032
SRA SRP223769

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
GSE138204_RAW.tar 173.1 Mb (http)(custom) TAR (of BW, TXT)
GSE138204_mgrA_DEGs_KB.txt.gz 489 b (ftp)(http) TXT
GSE138204_mgrA_DEGs_MM.txt.gz 1.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file

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