biostudies-arrayexpressMichael BarnesHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14509The Psoriasis Stratification to Optimise Relevant Therapy (PSORT) consortium, prospectively recruited deeply-phenotyped discovery and refinement psoriasis patient cohorts, during the early phase of treatment with two distinct biologics, adalimumab (TNF inhibitor) and ustekinumab (IL-12/23 inhibitor). Utilising this large multi-dimensional dataset, we aimed to identify transcripts associated with specific disease endotypes, defined by clinical and phenotypic features before commencing treatment (baseline); and disease severity endotypes, defined by Psoriasis Area and Severity Index (PASI)-associated gene expression profilesbiostudies-arrayexpressSequencing - sequencing of mRNA extracted from skin samples was performed at GSK Medicines Research Centre, Stevenage, UK using the Illumina HiSeq 2500 platformLibrary Construction - Libraries were prepared with the TruSeq Stranded Total RNA Sample Preparation Kits. The first step involved removal of ribosomal RNA (rRNA), conducted using biotinylated Ribo-Zero rRNA removal beads. For RNA extracted from skin, the Ribo-Zero Gold kit was used to deplete samples of cytoplasmic and mitochondrial rRNA.Sample Collection - Samples including lesional and non-lesional skin samples, were taken at each participant visit. Skin biopsies (6mm punch biopsies) were taken from lesional (edge of a plaque) and adjacent (minimum distance of 2cm) non-lesional skin from photoprotected sites on the lower back or upper buttock at each visit. Repeat biopsies were taken at a minimum distance of 2cm and biopsy sites were recorded.Nucleic Acid Extraction - mRNA was extracted from skin biopsies and whole blood using Qiagen Rneasy mini kitsOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Following RNA-seqencing of all samples, reads were pseudo-aligned using kallisto (Bray et al., 2016). Our reference genome was GRCh38.p10, Ensembl version 91. Transcript-level reads were aggregated to gene-level using the tximport package (Soneson et al., 2015). We provide the raw count matrix and normalised matrix. We merged counts with gene-level annotation data and remove probes with less than one count per million (CPM) in at least 20 libraries. This ensures that every probe is expressed in at least 5% of all samples. Counts are then TMM normalised prior to modelling (Robinson & Oshlack, 2010).UnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500RNA-seq of coding RNAHomo sapiensEstablishing an Academic-Industrial Stratified Medicine Consortium: Psoriasis Stratification to Optimize Relevant TherapyMichael BarnesNick ReynoldsChristopher E M Griffiths, Michael R Barnes, A David Burden, Frank O Nestle, Nick J Reynolds, Catherine H Smith, Richard B Warren, Jonathan N W N Barker, On Behalf Of The Psort ConsortiumfalseRNA-Seq study of skin and blood samples from prospectively-recruited, deeply-phenotyped discovery and refinement psoriasis cohorts, during targeted treatment with adalimumab or ustekinumabThe Psoriasis Stratification to Optimise Relevant Therapy (PSORT) consortium, prospectively recruited deeply-phenotyped discovery and refinement psoriasis patient cohorts, during the early phase of treatment with two distinct biologics, adalimumab (TNF inhibitor) and ustekinumab (IL-12/23 inhibitor). Utilising this large multi-dimensional dataset, we aimed to identify transcripts associated with specific disease endotypes, defined by clinical and phenotypic features before commencing treatment (baseline); and disease severity endotypes, defined by Psoriasis Area and Severity Index (PASI)-associated gene expression profiles2025-11-19T00:00:00Z2025-11-19T14:50:22.122Z2024-10-09T16:38:42.848ZE-MTAB-1450926569580EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_000418410.1038/jid.2015.286