Researchers have released a set of openly available RNA-seq datasets documenting how four freshwater bacterial isolates behave when iron becomes scarce. The data note, published in BMC Genomic Data on 6 August 2026, covers Pseudomonas sp. FBCC-B13192, Herbaspirillum sp. FBCC-B12834, Pantoea sp. FBCC-B5559 and Micrococcus sp. FBCC-B5738, each cultured under both FeCl3-treated and untreated conditions. Because bacteria respond to iron limitation by activating distinct uptake and siderophore-biosynthesis pathways, comparative transcriptomics under varying iron availability offers a window into these diverse adaptive mechanisms.
The dataset comprises eight paired-end sequencing libraries, corresponding to 16 FASTQ files, generated in 2024 and 2025 and totaling 349,853,404 processed reads. For every strain–condition combination, the authors prepared three biological replicate cultures, pooled their RNA and constructed a single sequencing library per combination. Raw sequence data are openly available in the NCBI Sequence Read Archive under SRA study accession SRP695241, within BioProject PRJNA1456794, spanning run accessions SRR38280322 through SRR38280329 and BioSamples SAMN57450602 through SAMN57450609.
Read alignment rates reported for the libraries varied considerably across strains. Pseudomonas sp. FBCC-B13192 achieved 78.59% under FeCl3-treated conditions and 71.98% under untreated conditions, while Herbaspirillum sp. FBCC-B12834 reached 92.30% and 89.11% respectively. Pantoea sp. FBCC-B5559 aligned at 89.29% and 89.23%, whereas Micrococcus sp. FBCC-B5738 showed markedly lower rates of 34.75% and 21.39% under treated and untreated conditions. Quality-control summaries, sample metadata and figure files are listed in Table 1 of the article and will be released through figshare.
The authors position the resource as a foundation for comparative analyses of bacterial iron-acquisition responses, noting that it also supports reanalysis with future transcriptome workflows. As a data note, the article describes the generation and availability of the datasets rather than presenting downstream biological conclusions, so any functional interpretation of the iron-response transcripts awaits independent analysis by the research community.
The article is open access, and the peer review reports are viewable alongside it.
Subject of Research: Transcriptome datasets of four freshwater bacterial isolates cultured under iron-replete and iron-limited conditions
Article Title: Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions
Article References: Hong, G. U., Gwak, Y. J., Hwang, Y., Jung, J. Y., & Lee, H. J. (2026). Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions. BMC Genomic Data, 27(1), Article 69. https://doi.org/10.1186/s12863-026-01477-9
Image Credits: AI Generated
DOI: 10.1186/s12863-026-01477-9
Keywords: RNA-seq, transcriptomics, freshwater bacteria, iron limitation, siderophores, Pseudomonas, Herbaspirillum, Pantoea, Micrococcus, NCBI Sequence Read Archive, data note, BMC Genomic Data
News Source: Juliet Wilcox. (October 30, 2026). Research report: Transcriptome datasets of four freshwater bacterial isolates grown under iron-replete and iron-limited conditions. Scienmag.
