biostudies-arrayexpressAlexandra SchmittHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15702Pancreatic ductal adenocarcinoma (PDAC) exhibits profound molecular heterogeneity and poor prognosis, necessitating novel tailored therapies. The basal and classical molecular subtypes of PDAC - driven by glycolysis versus lipid metabolism - have distinct prognostic implications. Spatial transcriptomics using FFPE tissue from 14 primary PDAC tumors was performed to spatially map PDAC molecular subtype heterogeneity. Our analysis resolved cancer cell signatures, deconvoluted intra-tumoral heterogeneity, and delineated a classical-to-basal trajectory.biostudies-arrayexpressSample Collection - Sections of 5µm thickness were cut from FFPE PDAC cancer tissueNucleic Acid Extraction - Nucleic acid extraction was performed according with The Visium Spatial Gene Expression for FFPE Kit (10X Genomics, PN-1000338) following the manufacturers instructionsLibrary Construction - The Visium Spatial Gene Expression for FFPE Kit (10X Genomics, PN-1000338) was used to generate sequencing libraries following the manufacturers instructionsSequencing - Libraries were sequenced using the DNBSEQ™ technology (BGI). Therefore, DNA Nanoballs (DNB) were created, and all samples were loaded on one flow cell using the DNBSEQ-G400 High-throughput Sequencing Set (BGI, 1000016970). Two samples were pooled together on one sequencing lane. The MGISEQ-2000 sequencer (BGI) was used with the following settings: Paired-end run, with 28 cycles for read1 (encoding spatial Barcode and UMI), 50 cycles for read2 (encoding the ligated probe insert), 10 cycles for i5 index and 10 cycles for i7 index (identifying each sample) (PE28 + 50 + 10 + 10). The sequencing depth was 300 Mio reads per lane, which equals a sequencing depth of 150 Mio reads per sample.MIAME ScoreOrganizationAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Normalization was applied to gene expression matrices. Spots passing quality-control filters were retained, and Seurat normalization was performed prior to downstream spatial clustering and visualization.Sequence Alignment - libraries were de-multiplexed, mapped to the human transcriptome (GRCh38 (2020-A)), and aligned to overlaying H&E images using SpaceRanger software with default settings (10X Genomics) and the manual alignment tool (LoupeBrowser v5.1.0, 10X Genomics)MetabolomicsUnknownTranscriptomicsGenomicsProteomicsDNBSEQ-G400spatial transcriptomics by high-throughput sequencingHomo sapiensAlexandra Schmittfalse14 primary formalin fixated paraffin embedded (FFPE) PDAC tissue slices from 14 patients without pretreatment were analyzed using spatial transcriptomicsPancreatic ductal adenocarcinoma (PDAC) exhibits profound molecular heterogeneity and poor prognosis, necessitating novel tailored therapies. The basal and classical molecular subtypes of PDAC - driven by glycolysis versus lipid metabolism - have distinct prognostic implications. Spatial transcriptomics using FFPE tissue from 14 primary PDAC tumors was performed to spatially map PDAC molecular subtype heterogeneity. Our analysis resolved cancer cell signatures, deconvoluted intra-tumoral heterogeneity, and delineated a classical-to-basal trajectory.2026-09-30T00:00:00Z2026-09-30T01:00:38.7Z2025-10-15T09:51:23.902ZE-MTAB-15702EFO_0002944EFO_0004170EFO_0030005EFO_0004917EFO_0005518EFO_0003816EFO_0004184