Comment[GEAAccession]	E-GEAD-460
MAGE-TAB Version	1.1
Investigation Title	Differential gene expression in the response to mytomycin C in Paracoccus denitrificans Pd1222
Experiment Description	In this project, RNA sequencing was performed to understand the mechanism to form membrane vesicles under DNA-damaging stress in Paracoccus denitrificans Pd1222.
Experimental Design	dose response design	genotype design
Experimental Factor Name	genotype	compound
Experimental Factor Type	genotype	compound
Person Last Name	Toyofuku
Person First Name	Masanori
Person Affiliation	University of Tsukuba
Person Roles	submitter
Public Release Date	2021-11-19
Protocol Name	P-GEAD-984	P-GEAD-985	P-GEAD-986	P-GEAD-987	P-GEAD-988
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	P. denitrificans Pd1222 wildtype and recA mutant were grown in TSB medium at an initial OD600 of 0.01 , after a 24 h incubation at 200 rpm.	Total RNA was isolated from the cell pellet using the SV Total RNA Isolation System (Promega, USA). Furthermore, we performed DNase treatment to remove residual total DNA using DNase I, recombinant, RNase-free solution (Roche, Switzerland).	The TruSeq Stranded Total RNA Library Preparation Kit (Illumina) and NEBNext rRNA Depletion Kit (Bacteria) (NEB).	NovaSeq 6000 system (Illumina).	Low-quality reads were removed and adapter trimming of the obtained raw FASTQ files were performed using fastp.  The cleaned FASTQ files were mapped to the P. denitrificans Pd1222 genome by using STAR. The number of reads mapped to each gene was counted using featureCounts.
SDRF File	E-GEAD-460.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB12561
Comment[Last Update Date]	2021-11-19