biostudies-arrayexpressJacqueline Tearle L. E.Homo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17162Mucosal pinch biopsies obtained during routine colonoscopies from two patients were subjected to BGI STOmics spatial transcriptomicsbiostudies-arrayexpressNucleic Acid Extraction - All samples were sectioned using the Leica CM1860 UV cryostat and two to three serial cuts were included on each Stereo-seq slide. Tissue sections were adhered to the Stereo-seq chip and incubated in -20°C methanol for 30 minutes. Stereo-seq slides were fluorescently stained with Qubit ssDNA Assay Kit (Q10212; ThermoFisher) as per the manual and imaged using a Leica DM6 microscope with a CTR6 LED electronics box. The Stereo-seq Permeabilisation Set for Chip-on-a-slide user manual (version B) was followed to obtain an optimal permeabilisation time for colonic mucosa tissue of 8 minutes.Sample Collection - Pinch biopsies were obtained during routine colonoscopies from one patient with ulcerative colitis (1x inflamed and 1x noninflamed region) and one patient with primary sclerosing cholangitis concomitant with colitis (noninflamed region only). Biopsies were embedded in optimal cutting temperature medium and fresh-frozen on dry ice.Library Construction - The cDNA was purified using SPRIselect Beads (B23318; Beckman Coulter). cDNA quality was quantified before and following cDNA library preparation using Qubit 4 fluorometer with Qubit dsDNA mix (Q33230; Invitrogen) and Agilent Tapestation High Sensitivity D5000 ScreenTape Assay (5067-5592 & 5067-5593; Agilent Technologies).Sequencing - cDNA libraries were pooled to a final concentration of 13.0 ng/µL (24.63 µL volume) and sequenced on one MGI G400 FCL PE100 flow cell at the South Australian Genomics Centre.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw FASTQ files were processed using the Stereo-seq Analysis Workflow (SAW) pipeline (BGI),, including spatial barcode decoding, genome alignment, UMI deduplication, tissue segmentation, generation of tissue-filtered gene expression matrices, and spatial clustering, to generate .gef filesUnknownTranscriptomicsGenomicsProteomicsNADNBSEQ-G400RNA-seq of coding RNAHomo sapiensJacqueline Tearle L. E.falseSTOmics spatial transcriptomics of ulcerative colitis and primary sclerosing cholangitis concomitant with colitis colonic mucosaMucosal pinch biopsies obtained during routine colonoscopies from two patients were subjected to BGI STOmics spatial transcriptomics2026-06-12T00:00:00Z2026-06-12T01:00:41.122Z2026-06-09T15:01:55.037ZE-MTAB-17162ERP194790EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184