biostudies-arrayexpressDavid LindgrenMus musculusspaceranger software (v2.0.1)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16421Two primary and two post-radiotherapy recurrent glioblastoma tumors derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium Spatial Gene Expression v1 chemistry.biostudies-arrayexpressSequencing - Final Visium spatial libraries were quantified by Qubit fluorometry and assessed using an Agilent Bioanalyzer. Libraries were pooled and sequenced on an Illumina NovaSeq 6000 using an SP 100-cycle kit v1.5, following Illumina recommendations for paired-end sequencing. Run configuration included PE100 for cDNA fragments and the appropriate index cycles required for Visium libraries.Sample Collection - Fresh tumors and healthy brain tissue were dissected from Nestin-Tv-a RCAS mice. Animals were sacrificed according to institutional ethical guidelines, and brains were rapidly dissected. Tumor and control brain regions were embedded in OCT on dry ice and snap-frozen in isopentane. Samples were stored at –80 °C until cryosectioning.Library Construction - Frozen tissue was cryosectioned at 10 µm on a pre-cooled cryostat and mounted onto 10x Genomics Visium Spatial Gene Expression Slides. Sections were fixed in ice-cold methanol, stained with hematoxylin and eosin (H&E), and imaged using a 10× objective including the fiducial frame. Permeabilization was performed for 21 minutes, based on prior optimization for this tissue type. Subsequent steps — second-strand synthesis, cDNA amplification, and library construction — were performed using the Visium Spatial Gene Expression Reagent Kit (10x Genomics, CG000239 Rev G) according to the manufacturer’s protocol.Nucleic Acid Extraction - For RNA quality control, 10 × 5 µm tissue sections from each tumor block were collected into microtubes and processed with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and integrity were assessed on an Agilent Bioanalyzer. Only samples with RIN > 8.8 were advanced to Visium library preparation.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw FASTQ files were processed using the 10x Genomics spaceranger software (v2.0.1). Reads were aligned to a custom mouse reference genome generated with Cell Ranger mkref, based on the mm10-2020-A reference (refdata-gex-mm10-2020-A) and extended with sequences encoding RCAS-derived transgenes (human PDGFB and RFP). Spatial barcode assignment and image alignment were performed using default parameters.Sequence Alignment - Raw FASTQ files were processed using the 10x Genomics spaceranger software (v2.0.1). Reads were aligned to a custom mouse reference genome generated with Cell Ranger mkref, based on the mm10-2020-A reference (refdata-gex-mm10-2020-A) and extended with sequences encoding RCAS-derived transgenes (human PDGFB and RFP). Spatial barcode assignment and image alignment were performed using default parameters.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNAMus musculusAlexander PietrasDavid LindgrenfalseSpatial transcriptomic profiling of primary and recurrent RCAS-derived glioblastoma in a mouse model using 10x Genomics Visium v1Two primary and two post-radiotherapy recurrent glioblastoma tumors derived in the RCAS/Nestin-Tv-a mouse model were processed using the 10x Genomics Visium Spatial Gene Expression v1 chemistry.2026-03-29T00:00:00Z2026-03-29T01:03:42.783Z2025-12-19T12:24:15.944ZE-MTAB-16421ERP186829E-MTAB-16420EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184