biostudies-arrayexpressfederica torricelliHomo sapiensGeoMx® Next-Generation Sequencing (NGS) Pipeline App (BaseSpace Illumina)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15378We compared GeoMX spatially resolved gene expression profiles of diffuse pleural mesothelioma (DPM) samples with or without somatic CDKN2A deletion. 5 CDKN2Adel and 4 WT DPM samples were analyzed. A total of 202 Areas Of Illumination (AOIs) were transcriptionally profiled, of which 140 Sarcomatoid-AOIs (S-AOIs) and 62 Epithelioid-AOIs (E-AOIs). Collectively, 97 AOIs belonged to WT DPM and 105 to CDKN2Adel DPMs.Profiling was performed using the GeoMx™Digital Spatial Profiler with Cancer Transcriptome Atlas panel.biostudies-arrayexpressSample Collection - Spatial transcriptomics was performed using the GeoMx® Digital Spatial Profiler (DSP) platform (NanoString Technologies) on 5 μm FFPE tumor tissue sections. To enable spatial selection, slides were stained with the GeoMx Solid Tumor TME Morphology Kit, which includes antibodies targeting cytokeratin (CK) and a nuclear stain (SYTO-13). Areas of interest (AOIs) were selected by two pathologists, who identified regions representative of tumor heterogeneity based on tissue morphology and Pan-CK expression. In biphasic tumors, both epithelioid and sarcomatoid regions were selected. Mixed regions were segmented to distinguish between epithelioid and sarcomatoid components.Sequencing - Prepared libraries were diluted to 1.6 pM and sequenced on an Illumina NextSeq 500 platform using a paired-end 2 × 27 bp configuration. Sequencing was performed with a target coverage of at least 30 reads per μm² of the collected AOI region.Nucleic Acid Extraction - Slides were hybridized with the GeoMx® Cancer Transcriptome Atlas panel, following the manufacturer’s protocol. After AOI selection and UV photo-cleavage of the barcoded probes, the released GeoMx RNA probes were collected and sequenced.Library Construction - Hybridized RNA probes were collected from each selected AOI, and next-generation sequencing (NGS) libraries were prepared using the GeoMx® Seq Code Pack (NanoString Technologies). Libraries were pooled based on AOI size, purified using AMPure XP beads (Beckman Coulter, Brea, California, USA), and resuspended in a volume proportional to the number of pooled AOIs. The quality and concentration of the library pools were assessed using Bioanalyzer (Agilent).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - After demultiplexing, FASTQ files were processed using the GeoMx® Next-Generation Sequencing (NGS) Pipeline App available on the BaseSpace Illumina Sequence Hub, which converted them into Digital Count Conversion (DCC) files. These DCC files were then uploaded to the GeoMx DSP platform and linked to their corresponding AOIs.Data Transformation - Initial quality control (QC) was performed on AOIs to assess sequencing performance, the number of nuclei collected, and background signal. Low-quality AOIs were excluded from downstream analysis. Subsequently, QC was applied to individual probes, and outlier probes were removed.UnknownTranscriptomicsGenomicsProteomicsNextSeq 500Nanostring GeoMx spatial profilerspatial transcriptomics by high-throughput sequencingHomo sapiensfederica torricellifalseGeoMX spatial transcriptomics of diffuse pleural mesothelioma: impact of CDKN2A deletionWe compared GeoMX spatially resolved gene expression profiles of diffuse pleural mesothelioma (DPM) samples with or without somatic CDKN2A deletion. 5 CDKN2Adel and 4 WT DPM samples were analyzed. A total of 202 Areas Of Illumination (AOIs) were transcriptionally profiled, of which 140 Sarcomatoid-AOIs (S-AOIs) and 62 Epithelioid-AOIs (E-AOIs). Collectively, 97 AOIs belonged to WT DPM and 105 to CDKN2Adel DPMs.Profiling was performed using the GeoMx™Digital Spatial Profiler with Cancer Transcriptome Atlas panel.2026-05-01T00:00:00Z2026-05-01T01:03:30.985Z2025-07-21T12:58:17.007ZE-MTAB-15378ERP176998EFO_0002944EFO_0004170EFO_0030005EFO_0004917EFO_0005518EFO_0003816EFO_0004184