title: GSM8686962: Slide1A_IntactMouseProstate_C57BL6_rep1; Mus musculus; OTHER
library_name: GSM8686962
library_construction_protocol: Slides in quadruplet on mice FFPE samples from two timepoints for a total of eight sections on two slides. Tissue sections of each sample type were analyzed for RNA integrity prior to placement on Spatial Tissue Optimization slides. Optimization was performed only for samples with RIN greater than or equal to 7. Spatial gene expression slides specific for either cryosections or FFPE sections were used (10X Genomics, Pleasanton, CA) and were submitted to the Advanced Genomics Core, (AGC, University of Michigan ILAB Core) for tissue optimization / permeabilization and Library Construction. Tissue was processed and placed the according to the manufacturer's instructions(CG000408 Visium Spatial Gene Expression for FFPE –Tissue Preparation Guide and CG000407 Visium Spatial Gene Expression for FFPE User Guide). Samples were stained lightly with H&E on the Spatial Gene Expression slides using a standard protocol CG000409 Visium Spatial Gene Expression for FFPE –Deparaffinization, H&E Staining, Imaging & Decrosslinkingand images scanned at high resolution and then probed with  the Visium Mouse Transcriptome Probe Set (Visium Mouse Transcriptome Probe Set v1.0). Visium sequencing depth for probe set assay was 100m reads/sample. All sequencing was performed at the University of Michigan Advanced Sequencing core on the NovaSeq6000 with 300 cycles and paired end 150. Each sequenced library was demultiplexed to FASTQ files and aligned to reads to the mm10 mouse transcriptomewith tr the Spatial Space Ranger 1.3