{"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-15020"],"description":["Small RNA sequencing was performed on 43 metachronous colorectal liver metastases (mCLM) and adjacent non-malignant liver tissue sample pairs to identify deregulated miRNAs. 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":["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.","Sample Collection - Metachronous colorectal liver metastasis tissue samples and their adjacent non-malignant liver tissues surgically resected from patients.","Sequencing - Sequenced on the NextSeq 2000 platform (Illumina Inc., CA, USA) using the P3 flow cell (1x72bp setting) and targeting 14 million reads per sample.","Library Construction - 1000 ng of total RNA was used for construction of small RNA libraries. The libraries were prepared using NEXTflex small RNA-Seq Kit v4 (PerkinElmer, Inc, Austin, USA), following the manufacturer’s 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["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.","Sequence Alignment - Quality control and trimming of raw small RNA sequencing data was performed using the Cutadapt v4.5. Reads shorter than 16 bp or longer than 28 bp were discarded. Potential rRNA sequences were identified and removed using SortMeRNA v2.1b. The remaining reads were aligned to the miRBase v22.1 reference sequence with BWA-backtrack using the following parameters of the aln function: -n 1 -o 0 -e 0 -k 1. The sequence counts were generated from mapped reads using the idxstats function in Samtools."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["microRNA profiling by high throughput sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Viktor Hlavac"],"additional_accession":[]},"is_claimable":false,"name":"MiRNome profiling in metachronous colorectal liver metastasis","description":"Small RNA sequencing was performed on 43 metachronous colorectal liver metastases (mCLM) and adjacent non-malignant liver tissue sample pairs to identify deregulated miRNAs. 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":"2026-01-13T14:31:16.377Z","creation":"2025-04-10T11:40:34.478Z"},"accession":"E-MTAB-15020","cross_references":{"ENA":["ERP171470"],"Biostudies":["E-MTAB-15022"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002896","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}