{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mariella Ferrante"],"organism":["Phaeodactylum tricornutum"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14821"],"description":["We generated a Phaeodactylum tricornutum strain in which the Nitrate Transporter 1/Peptide Transporter Family gene PtNPF2 was knocked out through the proteolistics CRISPR/Cas9 method. This strain was compared with a wild-type under normal pH conditions and after 24 hours from a shift from pH 8 to pH 7. The mutants showed a lag in growth coupled with impaired intracellular pH and photosynthetic performances."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Wild-type and Ptnpf2 KO cells were collected 24 hours after the shift to normal pH (pH 8) or low pH (pH 7), 18°C under white light at approximately 70 μmol photons m-2 s-1 and 12:12h, dark:light cycle. Around 10^8 cells were collected.","Nucleic Acid Extraction - RNA was extracted from cells with Trizol™ (Invitrogen), and the genomic DNA contamination was removed by DNase I treatment (RNase-Free DNase Set Qiagen) followed by RNA purification using Direct-zol™ RNA Microprep (ZYMO Research). RNA samples were quantified, and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA), as well as by running samples on a 1.5% agarose gel.","Library Construction - The TruSeq Stranded mRNA Library kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions. Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay.","Sequencing - Libraries were sequenced in paired-end 150 bp mode on NovaSeq 6000 (Illumina, San Diego, CA)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Cellular ion and pH homeostasis are crucial factors affecting and regulating metabolic reactions, protein stability, signalling and transport mechanisms. To balance intracellular ion concentrations, organisms need to constantly sense and respond to both the extracellular environment and cell compartments' requests. This fine-tuned system has been deeply studied in organisms, such as land plants and animals, but for diatoms, living in a highly variable environment, the key regulators of intracellular homeostasis have not yet been characterized. Previous results showed a pH response in the expression of the Phaeodactylum tricornutum NRT1/PTR Family transporter 2 (NPF2) gene, homologous to bacterial Proton-coupled Oligopeptide Transporters (POTs) involved in proton translocation across membra"],"study_type":["RNA-seq of total RNA"],"species":["Phaeodactylum tricornutum"],"pubmed_title":["NPF2 is involved in intracellular pH regulation and ion balance in the diatom Phaeodactylum tricornutum"],"pubmed_authors":["Mariella Ferrante","Santin, A., Russo, M.T., Croteau, D., Ruggiero, A., Russo Spena, S., Morales de los Rios, L., Corratge-Faillie, C., Brignone, S., Lacombe, B., Sanges, R., Chiurazzi, M., Ribera d'Alcalà, M., Bailleul, B., Falciatore, A., Ferrante, M.I. and Rogato, A."],"additional_accession":[]},"is_claimable":false,"name":"Gene expression analysis of a Phaeodactylum tricornutum wild-type strain and a knock-out strain for the Nitrate Transporter 1/Peptide Transporter Family gene PtNPF2","description":"We generated a Phaeodactylum tricornutum strain in which the Nitrate Transporter 1/Peptide Transporter Family gene PtNPF2 was knocked out through the proteolistics CRISPR/Cas9 method. This strain was compared with a wild-type under normal pH conditions and after 24 hours from a shift from pH 8 to pH 7. The mutants showed a lag in growth coupled with impaired intracellular pH and photosynthetic performances.","dates":{"release":"2026-08-28T00:00:00Z","modification":"2026-08-28T10:17:08.888Z","creation":"2025-02-06T19:32:33.384Z"},"accession":"E-MTAB-14821","cross_references":{"ENA":["ERP169028"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0004184"],"doi":["10.1111/nph.71169"]}}