title: GSM9618494: HP-F1 +cre breast tumor organoid transplanted cerebellum tumor slide; Mus musculus; OTHER
library_construction_protocol: Tumor tissues were fixed with 10% formalin, embedded in paraffin, and cut into 5-µm  sections. For H&E, slides were stained with hematoxylin, rinsed, and then counterstained with eosin, before being mounted and imaged. Tissue prepared for sectioning and staining starts with RNA quality assessment. RNA quality assessment of FFPE tissue blocks (RNA extraction and QC) need meets the DV200 Quality Score = >30% to proceed with assay using Agilent BioAnalyzer or TapeStation Instruments. Approved slides thickness at 5 μm sections compatible with the Visium CytAssist. 20x resolution imaging on Zeiss Axio Scan 7 Brightfield / Fluorescence Slide Scanner was used for downstream Space Ranger Analysis. Sample/Slide was prepared with decrosslinking and library Construction on 6.5mmx 6.5mm capture area. Visium CytAssist Spatial Gene Expression kit was used for FFPE (Mouse Transcriptome, 6.5 mm, 4 rxns, PN-1000521,10x Genomics). The probe processes include probe hybridization/Wash, probe ligation/Wash, RNA digestion and tissue removal, probe extension and elution, preamplification and cleanup and Index PCR. CytAssist Brightfield images generated for downstream Space Ranger Analysis. For sequencing information, 100M total read pairs was targeted for each sample on the Illumina NovaSeqX Plus instrument (NovaSeq X Plus 10B at 300 cycle, 10M targeted 2x150 Clusters).