{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Deborah F. Nacer"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16082"],"description":["The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions. Libraries were prepared using the Illumina TruSeq stranded mRNA protocol and sequenced on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden. Demultiplexing was performed using the bcl2fastq2 software v2.18.0.12 (Illumina) with default settings and the quality was checked with FastQC v0.11.3. Reads were mapped to the GRCh38 reference genome using the HISAT2 software v2.1.0 and annotation files from release 103. Finally, RNA-sequencing (RNA-seq) expression data in FPKM were calculated with StringTie v1.3.4d."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Lung adenocarcinoma samples were resected from patients that underwent surgery at the Skåne University Hospital in Lund, Sweden.","Library Construction - Libraries were prepared using the Illumina TruSeq stranded mRNA protocol.","Nucleic Acid Extraction - The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions.","Sequencing - Sequencing was performed on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Demultiplexing was performed using the bcl2fastq2 software v2.18.0.12 (Illumina) with default settings and the quality was checked with FastQC v0.11.3. Reads were mapped to the GRCh38 reference genome using the HISAT2 software v2.1.0 and annotation files from release 103. Finally, expression data in FPKM were calculated with StringTie v1.3.4d.","Data Transformation - Demultiplexing was performed using the bcl2fastq2 software v2.18.0.12 (Illumina) with default settings and the quality was checked with FastQC v0.11.3. Reads were mapped to the GRCh38 reference genome using the HISAT2 software v2.1.0 and annotation files from release 103. Finally, expression data in FPKM were calculated with StringTie v1.3.4d."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Multiomics assessment of lung adenocarcinoma subtypes defined through tumor purity-adjusted DNA methylation"],"pubmed_authors":["Johan Staaf","Deborah F. Nacer","Deborah F. Nacer, Elsa Arbajian, Srinivas Veerla, Mattias Aine, Mats Jönsson, Frida Rosengren, Anna Karlsson, Annette Salomonsson, Sofi Isaksson, Maria Planck, Johan Staaf"],"additional_accession":[]},"is_claimable":false,"name":"Processed RNA-seq of 95 lung adenocarcinoma samples","description":"The AllPrep DNA/RNA mini kit (Qiagen) was used for RNA extraction following manufacturer’s instructions. Libraries were prepared using the Illumina TruSeq stranded mRNA protocol and sequenced on the NovaSeq 6000 system at the Center for Translational Genomics (www.ctg.lu.se) in Lund, Sweden. Demultiplexing was performed using the bcl2fastq2 software v2.18.0.12 (Illumina) with default settings and the quality was checked with FastQC v0.11.3. Reads were mapped to the GRCh38 reference genome using the HISAT2 software v2.1.0 and annotation files from release 103. Finally, RNA-sequencing (RNA-seq) expression data in FPKM were calculated with StringTie v1.3.4d.","dates":{"release":"2026-02-08T00:00:00Z","modification":"2026-05-27T17:04:22.465Z","creation":"2025-11-13T14:45:59.241Z"},"accession":"E-MTAB-16082","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"],"doi":["10.1186/s13073-026-01609-x"]}}