{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Anda Gliga"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16322"],"description":["Renewable diesel fuels, derived from various biomass sources, have the potential to reduce greenhouse gas emissions and particulate matter (PM) compared to conventional fossil-based diesel. However, the toxicity of emissions from renewable diesel fuels is not yet fully understood.   We assessed pulmonary effects of renewable diesel exhaust particles in female C57BL/6Tac mice after a single pulmonary exposure via instatracheal instillation (6, 18, or 54 µg/mouse). Particles were generated from renewable fuels (rapeseed methyl ester, RME; hydrogen-treated vegetable oil, HVO) and petroleum diesel (DEP) using a modern heavy-duty diesel engine. Lung tissue was analysed via RNA sequencing one day post-exposure. Carbon black (Printex 90, 54 µg/mouse) was used as a particle control."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Lung tissue was collected 24 hours post exposure, snap-frozen in liquid nitrogen and stored at -80 until RNA extraction.","Nucleic Acid Extraction - Extraction of total RNA from lung tissue was performed using RNeasy Mini kit (Qiagen). One day prior to RNA extraction, tissues were placed in prechilled RNAlater®-ICE Frozen Tissue Transition Solution (Invitrogen) at -20 overnight. At the day of extraction, tissue was transferred to RLT buffer supplemented with B-mercaptoethanol (1 % v/v) and homogenized by a bead-homogenizer (Precellys 24) operated at 6500 rpm (20 seconds x 2). Subsequently, tissue lysate was transferred to QIA Shredder spin column (Qiagen, #74124) and centrifuged before supernatant was added to RNeasy column and total RNA was isolated according to manufacturer’s instructions with the inclusion of the purification step with DNase I (Qiagen).","Sample Treatment - Particles were suspended in Nanopure Diamond water with 0.1 % Tween80. An identical solution of Nanopure Diamond water with 0.1 % Tween80 served as vehicle control. A PFTE filter free from particles extracted with the same procedure was used as an extraction filter control. All solutions were freshly prepared and instilled within 1 h. Detailed description of the instillation protocol can be found in the reference below. For the downstream analysis the combustion particles should be compared to the extraction control (also containing vehicle) while the CB (Printex90) particles should be compared to the vehicle control since they are not combustion particles.   Bendtsen, K.M., Brostrøm, A., Koivisto, A.J. et al. Airport emission particles: exposure characterization and toxicity following intratracheal instillation in mice. Part Fibre Toxicol 16, 23 (2019). https://doi.org/10.1186/s12989-019-0305-5","Sequencing - Libraries were sequenced on an Illumina platform (PE150) at Novogene (Cambridge, United Kingdom).","Library Construction - RNA sequencing libraries were prepared using Illumina’s standard stranded mRNA library preparation protocol with poly(A) enrichment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - To adjust for sequencing depth data was transformed to cpm, counts per million. This was the input used for the differential gene expression analysis.","Sequence Alignment - For alignment, the reference genome index was constructed using HISAT2 v2.0.5. Paired-end clean reads were mapped to the reference genome with HISAT2 v2.0.5 under default parameters. Gene-level read counts were obtained using featureCounts v1.5.0-p3, which quantified the number of reads uniquely mapped to each gene."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_title":["Similar global transcription patterns in mouse lung tissue following pulmonary exposure to renewable and conventional diesel engine exhaust particles."],"pubmed_authors":["Gliga AR, McCarrick S, Malmborg V, Kohonen P, Snigireva A, Mills B, Danielsen PH, Palmberg L, Broberg K, Pagels J, Vogel U.","Anda Gliga"],"additional_accession":[]},"is_claimable":false,"name":"RNAseq of lung tissue from mice exposed to conventional and renewable diesel exhaust particle","description":"Renewable diesel fuels, derived from various biomass sources, have the potential to reduce greenhouse gas emissions and particulate matter (PM) compared to conventional fossil-based diesel. However, the toxicity of emissions from renewable diesel fuels is not yet fully understood.   We assessed pulmonary effects of renewable diesel exhaust particles in female C57BL/6Tac mice after a single pulmonary exposure via instatracheal instillation (6, 18, or 54 µg/mouse). Particles were generated from renewable fuels (rapeseed methyl ester, RME; hydrogen-treated vegetable oil, HVO) and petroleum diesel (DEP) using a modern heavy-duty diesel engine. Lung tissue was analysed via RNA sequencing one day post-exposure. Carbon black (Printex 90, 54 µg/mouse) was used as a particle control.","dates":{"release":"2026-03-13T00:00:00Z","modification":"2026-03-13T17:29:34.192Z","creation":"2025-11-28T15:38:57.474Z"},"accession":"E-MTAB-16322","cross_references":{"pubmed":["publ-0-7202-removable"],"ENA":["ERP185805"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"],"doi":["10.1016/j.etap.2025.104918"]}}