{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["sunghee park"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15494"],"description":["The objective of this study is to investigate the compositional differences in the bile microbiota between malignant (BTC) and benign biliary conditions, in order to gain new insights into the pathogenesis of biliary tract cancer."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Sequencing was conducted on the Illumina MiSeq platform (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. Raw sequencing reads were processed using QIIME2 (v2022.2). Quality filtering, denoising, and chimera removal were performed using the DADA2 algorithm, which also produced amplicon sequence variants (ASVs) through dereplication. Reads were trimmed to 282 bp (forward) and 239 bp (reverse).  A total of 5,927,608 16S rRNA sequences were obtained from 59 individual samples, resulting in 6,547 distinct features and an average of 100,467 sequences per sample. The resulting ASV table was used for taxonomic classification, diversity analyses, and differential abundance testing. Taxonomy was assigned using the SILVA database (v138) with a scikit-learn-based classifier. Sequencing and data analysis were performed by referring to the Wensel et al. (2025) [8], paper and modifying it with appropriate methods.","Sample Collection - We enrolled 143 patients at Pusan National University Hospital between May 2021 and December 2023, including 56 patients diagnosed with BTCs and 87 with BBDs. A total of 84 patients were excluded because of their unsuitability for sequencing analysis. Clinical data and bile samples were collected during surgery or endoscopic retrograde cholangiopancreatography (ERCP). All bile samples obtained during ERCP were collected using a new catheter prior to the endoscopic sphincterotomy (EST) after guide wire-assisted cannulation only in cases in which the ampullary orifice was patented. Samples were aspirated using syringe suction before the administration of contrast agents. A minimum of 5 mL of bile was collected, and efforts were made to collect 10 mL or more whenever feasible. Fresh bile samples were immediately stored at -80°C after collection, 1 mL aliquots were divided into separate tubes for subsequent analysis. (IRB approval no. 2105-004-102)","Nucleic Acid Extraction - Frozen 1 mL bile juice sample were thawed, and microbiome DNA was extracted using the QIAamp DNA Microbiome Kit according to the manufacturer's instructions. The extracted microbiome DNA was eluted in 50 µL of the kit’s elution buffer and stored at -20°C until further analysis.","Library Construction - The V3–V4 regions of the 16S rRNA gene were PCR-amplified using barcoded universal primers."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The resulting ASV table was used for taxonomic classification, diversity analyses, and differential abundance testing. Taxonomy was assigned using the SILVA database (v138) with a scikit-learn-based classifier."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina MiSeq"],"study_type":["DNA-seq"],"species":["Homo sapiens"],"pubmed_authors":["sunghee park"],"additional_accession":[]},"is_claimable":false,"name":"Differences in the biliary microbiome between biliary tract cancer and benign biliary disease","description":"The objective of this study is to investigate the compositional differences in the bile microbiota between malignant (BTC) and benign biliary conditions, in order to gain new insights into the pathogenesis of biliary tract cancer.","dates":{"release":"2025-08-30T00:00:00Z","modification":"2025-08-30T01:01:57.474Z","creation":"2025-08-14T10:21:37.668Z"},"accession":"E-MTAB-15494","cross_references":{"ENA":["ERP178764"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"]}}