biostudies-arrayexpressMelina SchöpkerRaphidocelis subcapitatahttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16813n the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the zinc oxide nanoparticle NM-110. R. subcapitata was exposed to the ZnO NP NM-110 according to OECD guidelines (OECD test No. 201). At the end of exposure time (72 hours), simultaneous RNA and protein extraction was performed using a newly established RNA extraction protocol combinded with the Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Novaseq6000 system with a read length of 150 base pairs in paired-end run mode and the obtained sequences went through bioinformatic analysis pipeline to identify and count the detected gene sequences followed by differential gene expression analysis and overrepresentation analysisbiostudies-arrayexpressSequencing - Illumina Novaseq6000 sequencing system was employed to obtain 30 million read pairs with a read length of 150 base pairs in paired-end run modeLibrary Construction - RNA libraries were prepared from RNA extracts and the TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, USA)Sample Collection - At the end of exposure, 50 ml of algae suspension was centrifuged, the cell pellets immersed in liquid nitrogen for at least 3 min and dried in open reaction tube in a SpeedVac vacuum centrifuge (Thermo Fisher Scientific, Waltham, USA) at 43 °C for 30-60 min. The cell pellets were then homogenised in lysis buffer using 0.1 mm glass beads and the FastPrep-24 homogeniser (MP Biomedicals, Santa Ana, USA) at 5 m/s speed for 2x2 minutes.Sample Treatment - three replicates (100 ml each) were exposed to each of two sub-lethal concentrations of the ZnO NP NM-110 (high exposure and low exposure concentrations) in addition to untreated control groups.Nucleic Acid Extraction - Simultaneous RNA and protein extraction was performed from the homogenised samples using an adapted extraction protocol based on the Macherey & Nagel RNA/protein extraction kitGrowth Protocol - Algae were exposed to the Zno NP NM-110 for 72 hours according to OECD test guidelines No. 201 at 22 ± 2 °C under continuous illumination with a light intensity of 60-120 µE∙m-2∙s-1OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw sequencing data were pre-processed with fastp (v0.23.2) to remove adapters and low quality reads. Quality assessment was performed using FastQC (v0.11.9), potential contaminants were screened with FastQ Screen (v0.15.3) and results were aggregated with MultiQC (v1.12). Reads were mapped to the R. subcapitata reference genome Rsub_1.0, and quantified using STAR (v2.7.5b).Data Transformation - Differentially expressed genes (DEG) were identified using DESeq2 (v1.46.0) in R (v4.4.1). Prior to analysis, genes were filtered using a relevance threshold criterion, retaining only genes with >1 CPM in at least two replicates in at least one experimental condition.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNARaphidocelis subcapitataKarsten SchlichFabian EssfeldMelina SchöpkerSebastian EilebrechtBenedikt RingbeckfalsemRNA-Seq of R. subcapitata exposed to different concentrations of the zinc oxide nanoparticle NM-110 against untreated control groupsn the present study transcriptome analysis was employed to investigate the early molecular responses to exposure to the zinc oxide nanoparticle NM-110. R. subcapitata was exposed to the ZnO NP NM-110 according to OECD guidelines (OECD test No. 201). At the end of exposure time (72 hours), simultaneous RNA and protein extraction was performed using a newly established RNA extraction protocol combinded with the Macherey & Nagel RNA/protein extraction kit. The obtained RNA extracts were sequenced using Novaseq6000 system with a read length of 150 base pairs in paired-end run mode and the obtained sequences went through bioinformatic analysis pipeline to identify and count the detected gene sequences followed by differential gene expression analysis and overrepresentation analysis2026-04-15T00:00:00Z2026-04-17T01:01:33.597Z2026-03-26T11:07:19.013ZE-MTAB-16813ERP191365EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969