{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR671/000/SRR6710140/SRR6710140_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR671/009/SRR6710139/SRR6710139_2.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR671/009/SRR6710139/SRR6710139_1.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR671/000/SRR6710140/SRR6710140_1.fastq.gz"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Wuhan University"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA433851"],"scientific_name":["Pseudomonas fluorescens"],"tag":["xref:PubMed:29531068"],"long_description":["To determine whether PT modifications are involved in the epigenetic control of specific genes, RNA-seq analysis was conducted to define global transcriptional changes in early log-phase cultures of wild-type pf0-1 and the PT modifacation related genes(dndBCDE) deletion mutant TT-5. Compared with wild-type pf0-1, a total of ten genes in TT-5 exhibited differential expression of greater than 2-fold (log2-ratio>1 or <-1, p-value<0.05, FDR≤0.001), including 6 up-regulated genes and 4 down-regulated genes (Table 1). Compared with pf0-1, the most significantly downregulated genes were dndBCDE themselves due to the in-frame deletion in TT-5. Of the 6 up-regulated genes, two are phage-related proteins (Pfl01_1169 and Pfl01_3496) the rest are genes encoding a putative membrane protein (Pfl01_0900), xanthine dehydrogenase (Pfl01_1797), N-acetylmuramoyl-L-alanine amidase (Pfl01_5657) and a hypothetical protein (Pfl01_2488). The transcription levels of the differentially expressed genes varied to different degrees and the genes belong to different COG groups. Overall design: Examination of global transcriptional variation in wild type P. fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant"],"repository":["ENA"],"additional_accession":[]},"is_claimable":false,"name":"Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis","description":"Definition of global transcriptional variation in wild type Pseudomonas fluorescens Pf0-1 and its phosphorothioate modification (PT) deficient mutant by RNA-seq analysis","dates":{"last_updated":"2025-09-24","first_public":"2018-03-01"},"accession":"PRJNA433851","cross_references":{"GEO":["GSE110489"],"taxon":["294"],"PubMed":["29531068"]}}