{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Viktor Hlavac"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15022"],"description":["Differential expression analysis was performed on 36 metachronous colorectal liver metastases (mCLM) and adjacent non-malignant liver tissue sample pairs to identify deregulated genes. GSEA and CMS classification were used to explore pathways and stratify tumors. miRNA-mRNA interactions were investigated through co-expression and correlation analysis, with prognostic relevance assessed by survival analysis. This study gave a holistic view of the molecular landscape of mCLM and revealed key deregulated pathways and novel miRNA-mRNA interactions with potential prognostic implications."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequenced on the NextSeq 500 platform (Illumina Inc., CA, USA) using the High Output kit (1x75bp setting) and targeting 5 million reads per sample.","Nucleic Acid Extraction - Total RNA was extracted from tumor tissue using the TRIZOL reagent (Thermofisher) following the manufacturer’s protocol. The tissue was first pulverized with mortar and pestle under liquid nitrogen.","Library Construction - 500 ng of total RNA was used for construction of RNA libraries. The cDNA libraries corresponding to mRNA were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s protocol. Samples with RIN>3.5 (n=72) were processed by the standard protocol, while samples with RIN<3.5 (n=14) were processed using the Low Quality RNA protocol. Quality of prepared libraries was checked by Tapestation 2200 using High Sensitivity D1000 kit (Agilent Technologies Inc., CA, USA) and quantity measured by the Qubit instrument using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific, MA, USA). Prepared libraries were pooled equimolarly.","Sample Collection - Metachronous colorectal liver metastasis tissue samples and their adjacent non-malignant liver tissues surgically resected from patients."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Quality control and trimming of raw RNA sequencing data was performed using the fastp package v0.23.4. For annotation, reference transcriptome Ensembl v110 (GRCh38) was used using STAR aligner v2.7.5c. The quality of the aligned reads was assessed with the RSeQC package. Read quantification was conducted in the Rsubread (R/Bioconductor) v2.20.0.","Data Transformation - The count normalization and differential expression analysis was conducted using the DESeq2 package (R/Bioconductor) v1.46.0.  For correlation analyses, the data were log2 scaled."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Viktor Hlavac"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq profiling in metachronous colorectal liver metastasis","description":"Differential expression analysis was performed on 36 metachronous colorectal liver metastases (mCLM) and adjacent non-malignant liver tissue sample pairs to identify deregulated genes. GSEA and CMS classification were used to explore pathways and stratify tumors. miRNA-mRNA interactions were investigated through co-expression and correlation analysis, with prognostic relevance assessed by survival analysis. This study gave a holistic view of the molecular landscape of mCLM and revealed key deregulated pathways and novel miRNA-mRNA interactions with potential prognostic implications.","dates":{"release":"2026-01-12T00:00:00Z","modification":"2026-01-12T15:15:50.113Z","creation":"2025-04-10T11:43:17.111Z"},"accession":"E-MTAB-15022","cross_references":{"ENA":["ERP171471"],"Biostudies":["E-MTAB-15020"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}