{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110489/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Pseudomonas fluorescens"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110489"],"repository":["GEO"],"entry_type":["GSE"],"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":"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.","dates":{"publication":"2018/02/15"},"accession":"GSE110489","cross_references":{"GSM":["GSM2992351","GSM2992350"],"GPL":["24598"],"SRA":["SRP132712"],"GSE":["110489"],"taxon":["Pseudomonas fluorescens"],"PMID":["[29531068]"]}}