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Series GSE112354 Query DataSets for GSE112354
Status Public on Mar 27, 2018
Title Transcriptome analysis of gene expression of PAK-AR2 and 1-9
Organism Pseudomonas aeruginosa
Experiment type Expression profiling by high throughput sequencing
Summary RNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false discovery rate (FDR ) ≤ 0.001, fold change |log2Ratio|≥1.A total of 4,355,305 reads matched to the referenced genome in the sample of PAK-AR2, and 3,544,484 reads in the sample of 1-9.Transcriptome data showed that expression of 361 genes were upregulated while 459 genes were down regulated by at least 2-fold when comparing the srpA mutant strain 1-9 to its parent strain PAK-AR2.These genes were classified into 21 major cellular processes based on the annotation of KEGG_B_class or further grouped into several major metabolic pathways, such as ribosomal proteins, type III secretion system (T3SS), type VI secretion system (T6SS), chemotaxis, cell motility, and cell shape control.More and more small proteins that were ignored from typical genome annotations have now been experimentally demonstrated to play important regulatory roles on various bacterial metabolic.
 
Overall design Gene expression of PAK-AR2 and 1-9 were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.
 
Contributor(s) You J, Yang H
Citation(s) 29748556
Submission date Mar 26, 2018
Last update date Jun 27, 2018
Contact name jia jia You
E-mail(s) jiajiayouhnlg2014@163.com
Organization name Tianjin University of Science & Technology
Department College of Biotechnology
Lab Key Laboratory of Industrial Microbiology
Street address 29 13th Street, TEDA
City Tianjin
ZIP/Postal code 300457
Country China
 
Platforms (1)
GPL18644 Illumina HiSeq 2000 (Pseudomonas aeruginosa)
Samples (2)
GSM3068268 PAK_AR2A
GSM3068269 s1_9A
Relations
BioProject PRJNA445735
SRA SRP136496

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
GSE112354_PAK_AR2A-VS-s1_9A.GeneDiffExp.txt.gz 472.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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