biostudies-arrayexpressDavid LindgrenMus musculusspaceranger (v4.0.1, 10x Genomics)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16420One healthy mouse brain and one glioblastoma tumor derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium HD Spatial Gene Expression chemistry.biostudies-arrayexpressSample Collection - Mouse brain tissue (one healthy and one RCAS-derived glioma) was collected and post-fixed in 4% paraformaldehyde for 24 hours, dehydrated, and embedded in paraffin. Sections of 3 µm thickness were cut from the FFPE blocks and mounted onto standard glass slides for histological preparation and subsequent spatial transcriptomic processing.Sequencing - Visium HD spatial gene expression libraries were sequenced on an Illumina platform following the manufacturer’s recommendations for Visium HD library specifications. Raw FASTQ files were generated for downstream processing using 10x Genomics spaceranger software.Library Construction - Tissue sections mounted on glass slides were H&E stained prior to hybridization. Probe hybridization was performed using the Visium Mouse Transcriptome Probe Set v2.0 (mm10-2020-A), supplemented with custom-designed probes targeting RCAS-derived transgenes (one probe for human PDGFB and two probes for RFP). Following hybridization, slides were processed using the Visium CytAssist instrument to transfer probe-labeled tissue onto Visium HD slides.Nucleic Acid Extraction - RNA quality was assessed from each FFPE block by processing ten 5 µm sections using the RNeasy FFPE Kit (Qiagen 73504). Extracted RNA was analyzed on an Agilent Bioanalyzer to determine DV200 values and confirm that they met the recommended threshold for Visium HD spatial transcriptomics.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw FASTQ files were processed with spaceranger (v4.0.1, 10x Genomics) using a custom Visium HD reference composed of the mm10-2020-A genome and Visium Mouse Transcriptome Probe Set v2.0 extended with custom probes targeting human PDGFB and RFP.Sequence Alignment - Raw FASTQ files were processed with spaceranger (v4.0.1, 10x Genomics) using a custom Visium HD reference composed of the mm10-2020-A genome and Visium Mouse Transcriptome Probe Set v2.0 extended with custom probes targeting human PDGFB and RFP.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAMus musculusAlexander PietrasDavid LindgrenfalseSpatial transcriptomic profiling of healthy brain and RCAS-derived glioblastoma in a mouse model using 10x Genomics Visium HDOne healthy mouse brain and one glioblastoma tumor derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium HD Spatial Gene Expression chemistry.2026-03-29T00:00:00Z2026-03-29T01:03:42.779Z2025-12-19T11:50:27.16ZE-MTAB-16420ERP186828E-MTAB-16421EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184