Project description:The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of Pseudomonas aeruginosa PAO1 in response to 0, 1, 20 and 25 mg/L AgNPs or 0, 1,30 and 300 mg/L AgNRs for 2 h, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Project description:This study provides comparative RNA-seq datasets for four freshwater bacterial isolates, Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559, and Micrococcus sp. FBCC-B5738, cultured under iron-replete (+100 uM FeCl3) and iron-limited (no FeCl3) conditions. Iron availability is a key factor influencing bacterial fitness, and iron limitation is known to activate siderophore biosynthesis, iron transport, and homeostasis pathways. A total of eight libraries generated in 2024 and 2025 were analyzed, comprising 349.9 million processed reads. Reference-guided mapping rates varied among strains, with higher mapping efficiency observed in Pseudomonas, Herbaspirillum, and Pantoea, while Micrococcus showed comparatively lower mapping rates under both conditions. Differential expression analysis revealed strain-specific responses to iron limitation. Genes related to pyoverdine and ferrichrome uptake were enriched in Pseudomonas and Herbaspirillum, enterobactin-associated pathways were prominent in Pantoea, and genes associated with siderophore production, heme utilization, and Fe-S cluster assembly were identified in Micrococcus. Raw sequencing data are available in the NCBI Sequence Read Archive under BioProject PRJNA1456794, and processed data are deposited in a public repository. These datasets provide a valuable resource for understanding bacterial adaptation to iron availability and for comparative transcriptomic analyses.