{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Sara Al-Badran"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15349"],"description":["FFPE polyp tissue from bowel screening patients removed by polypectomy in Glasgow, UK between 2009-2016 underwent targeted sequencing using TempO-Seq (carried out by BioClavis Ltd.), as part of the INCISE collaborative. TempO-Seq™ (Biospyder Technologies, Carlsbad, CA, USA) whole transcriptome profiling was performed on patients from the INCISE cohort, according to the manufacturer’s instructions using whole FFPE tissue sections. Only unnormalized raw counts were provided by BioClavis."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - INCISE FFPE tissue full sections were cut to be 4μm thick and mounted on glass slides.","Sequencing - Single library was run on the Illumina MiniSeq High-Output flowcell. Sequencing reads were demultiplexed by BCL2FASTQ software (Illumina, USA). BioClavis only provided unnormalized raw counts.","Nucleic Acid Extraction - To generate lysates, the full FFPE tissue was scraped off and placed in 1x FFPE Lysis Buffer (BioSpyder), and deparaffinised. Further processing included incubation in FFPE Protease (BioSpyder), followed by mechanical homogenization by trituration.  Detector oligo hybridization, digestion, and ligation, and subsequent PCR amplification was performed using a unique primer set for each sample, introducing a sample-specific barcode and Illumina adaptors according to manufacturer’s instructions.","Library Construction - Barcoded PCR products was added to a flip-spin reservoir and purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit (Cat. 740609.50, Macherey-Nagel) and quantified by Qubit using the dsDNA kit (Cat. Q32851, ThermoFisher Scientific), to generate a single library."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Normalised counts were generated using quantile normalisation and log2 +1 transformed."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina MiniSeq"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Joanne Edwards","Sara Al-Badran"],"additional_accession":[]},"is_claimable":false,"name":"Templated Oligo Sequencing (TempO-Seq) of FFPE Polyp Tissue from Patients in the Scottish Bowel Screening Program","description":"FFPE polyp tissue from bowel screening patients removed by polypectomy in Glasgow, UK between 2009-2016 underwent targeted sequencing using TempO-Seq (carried out by BioClavis Ltd.), as part of the INCISE collaborative. TempO-Seq™ (Biospyder Technologies, Carlsbad, CA, USA) whole transcriptome profiling was performed on patients from the INCISE cohort, according to the manufacturer’s instructions using whole FFPE tissue sections. Only unnormalized raw counts were provided by BioClavis.","dates":{"release":"2025-07-31T00:00:00Z","modification":"2025-07-29T12:12:40.692Z","creation":"2025-07-07T09:46:00.069Z"},"accession":"E-MTAB-15349","cross_references":{"ENA":["ERP177387"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}