{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Zehao Guo"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15886"],"description":["This dataset contains processed RNA sequencing expression matrices derived from osteosarcoma patient samples. A total of 40 clinical specimens were analyzed, including 30 primary osteosarcoma tumor tissues and 10 non-sarcoma tissues. Raw sequencing data were preprocessed to generate normalized gene expression matrices suitable for downstream bioinformatic analyses, such as differential expression and pathway enrichment studies."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Tumor and non-malignant tissue samples were collected from patients.Samples were immediately snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.All sample collection procedures were approved by the local ethics committee, and informed consent was obtained from all patients.","Nucleic Acid Extraction - Total RNA was extracted from frozen tissue using the TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA integrity was assessed using the Agilent 2100 Bioanalyzer, and samples with RNA integrity number (RIN) ≥ 7 were used for library preparation. RNA concentrations were measured using a NanoDrop spectrophotometer.","Library Construction - RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions.Poly(A) mRNA was enriched from total RNA and fragmented, followed by first- and second-strand cDNA synthesis. Libraries were indexed, PCR-amplified, and purified, with an average fragment size of approximately 300 bp (SDev ~30–50 bp). Libraries were non-stranded (unstranded) and prepared for paired-end sequencing (orientation inward, 5335).","Sequencing - Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads. Sequencing reads were processed and mapped to the human reference genome (GRCh38). Gene-level expression matrices were generated using standard pipelines, and normalized counts were used for downstream analysis. Only processed expression matrices were submitted; raw FASTQ files are not available."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw read counts obtained from RNA-seq experiments were processed to generate the submitted expression matrix. Quality control was performed on the raw reads using FastQC to assess sequence quality, adapter contamination, and duplication levels, followed by trimming of low-quality bases and adapters using Trimmomatic. Cleaned reads were aligned to the reference genome (GRCh38/hg38) using STAR with default parameters, and gene-level counts were quantified using featureCounts based on GENCODE v39 annotation. Genes with low expression were filtered out, and the remaining counts were normalized using the variance-stabilizing transformation (VST) implemented in DESeq2 to account for differences in library size and composition."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Thermal cycler, Magnetic stand / beads, Pipettes and tips, Microcentrifuge tubes, Plate shaker","Liquid nitrogen, -80°C freezer, Surgical tools (scalpels, forceps), Sample tubes / cryovials","Illumina NovaSeq 6000","Centrifuge, Pipettes and tips, Agilent 2100 Bioanalyzer, NanoDrop spectrophotometer, Vortex mixer","None"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Zehao Guo"],"additional_accession":[]},"is_claimable":false,"name":"Osteosarcoma patient RNA sequencing data matrix","description":"This dataset contains processed RNA sequencing expression matrices derived from osteosarcoma patient samples. A total of 40 clinical specimens were analyzed, including 30 primary osteosarcoma tumor tissues and 10 non-sarcoma tissues. Raw sequencing data were preprocessed to generate normalized gene expression matrices suitable for downstream bioinformatic analyses, such as differential expression and pathway enrichment studies.","dates":{"release":"2025-11-21T00:00:00Z","modification":"2026-06-01T03:45:23.343Z","creation":"2025-10-29T16:27:06.097Z"},"accession":"E-MTAB-15886","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}