biostudies-arrayexpressCarl-Eric WegnerBeijerinckiaceae bacteriumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15640We investigated lanthanide (Ln) utilization in Beijerinckiaceae bacterium RH AL1, which requires light Lns (La–Nd) for methanol oxidation. The strain was grown with methanol as the carbon and energy source and with Ln sources including natural minerals (apatite, bastnäsite, gadolinite, loparite, monazite, xenotime), an alloy (ferrocerium), and synthetic compounds (La₂O₃, Nd₂O₃, LaPO₄). We did two rounds of incubations and cultures were grown to mid-exponential phase. Total RNA was extracted and mRNA enriched by means of subtractive hybridization, before samples were subjected to sequencing library preparation for downstream Illumina high-throughbut sequencing. Pre-processed and trimmed data was subsequently used for differential gene expression analysis.biostudies-arrayexpressGrowth Protocol - Beijerinckiaceae bacterium RH AL1 was grown using MM2 medium to mid-exponential phase, using methanol (0.5%, v/v; 123 mM) as carbon and energy source.Sequencing - An equimolar pool of libraries was subjected to Illumina sequencing (2 x 100 bp, paired ends) with an NovaSeq 6000 instrument and a SP flowcell (Illumina, San Diego, California, USA). Sequencing was carried out by the sequencing core facility of the Leibniz Institute on Aging - Fritz Lipmann Institute.Nucleic Acid Extraction - Total RNA was extracted with TRI reagent (Applied Biosystems), mRNA was enriched using the RiboMinus bacteria 2.0 transcriptome isolation kit (Invitrogen).Sample Collection - Biomass was harvested from mid-exponential cultures by means of centrifugation.Library Construction - Sequencing libraries were prepared with the NEBNext Ultra II Directional RNA library prep kit for Illumina (New England Biolabs).Sample Treatment - Cultures were supplemented with either different lanthanum compounds (LaCl3, La2O3, LaPO4; 1 µM total lanthanum) or lanthanide-containing minerals/alloys as lanthanide source. The following minerals/alloys have been used: bastnaesite, gadolinite, loparite, monazite, xenotime, ferrocerium. For incubations with ferrocerium one piece of ferrocerium (~ 145 mg) was added. For incubations with a mineral lanthanide source, we used 5 mg of the respective mineral.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Quality of raw and later trimmed data was assessed with FastQC (v0.11.9). Adaptor- and quality-trimming was carried out with bbduk (v38.26) (settings: minlen= 75, qtrim = rl, ktrim = rl, k = 25, mink= 11, trimq = 20, qtrim = rl). Trimmed reads were filtered with SortMeRNA (v2.1) to remove rRNA-derived and non-coding RNA sequences. The number of mapped reads per feature (e.g. coding genes) was determined from .bam files that have been sorted and indexed with samtools (v1.3.1) using featureCounts, which is part of the Subread package (v1.6.3).Sequence Alignment - Read mapping onto the available reference genome of Beijerinckiaceae bacterium RH AL1 was done with bbmap (v.38.26) (settings: slow, k = 11). The number of mapped reads per feature (e.g. coding genes) was determined from .bam files that have been sorted and indexed with samtools (v1.3.1) using featureCounts, which is part of the Subread package (v1.6.3).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNABeijerinckiaceae bacteriumCarl-Eric WegnerfalseGene expression dynamics in Beijerinckiaceae bacterium RH AL1 in response to different lanthanum compounds and different lanthanide-containing mineralsWe investigated lanthanide (Ln) utilization in Beijerinckiaceae bacterium RH AL1, which requires light Lns (La–Nd) for methanol oxidation. The strain was grown with methanol as the carbon and energy source and with Ln sources including natural minerals (apatite, bastnäsite, gadolinite, loparite, monazite, xenotime), an alloy (ferrocerium), and synthetic compounds (La₂O₃, Nd₂O₃, LaPO₄). We did two rounds of incubations and cultures were grown to mid-exponential phase. Total RNA was extracted and mRNA enriched by means of subtractive hybridization, before samples were subjected to sequencing library preparation for downstream Illumina high-throughbut sequencing. Pre-processed and trimmed data was subsequently used for differential gene expression analysis.2026-02-01T00:00:00Z2026-02-01T02:02:25.828Z2025-09-29T12:04:50.766ZE-MTAB-15640ERP180761EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969