GSM8305661: Visium, Irf3EC Day 3 MI (V52) biol rep1; Mus musculus; RNA-Seq
Sections obtained from mice were imaged and processed for spatially resolved gene expression using the Visium Spatial Transcriptomics kit for Fresh/Frozen samples (10x Genomics). Samples were immediately snap-frozen in OCT using isopentane that was cooled in a liquid nitrogen bath. For cryosectioning, samples were equilibrated to −22 °C. 10 μm thick short axis sections were cut from the blocks onto Visium slides (10X Genomics) and processed according to the manufacturer's protocol. Tissue permeabilization time was optimized at 30 minutes for infarcted mouse hearts. Hematoxylin and eosin (H&E) images generated during the Visium protocol were captured at 20x magnification on Nikon Eclipse Ti2-E widefield microscope and exported as tiled tiffs for analysis. Libraries were sequenced on the Illumina NovaSeq platform, and resulting data were processed using SpaceRanger (v.1.2.2, 10X Genomics) Single-nucleus RNA-seq was performed by microfluidic droplet-based encapsulation, barcoding, and library preparation, (10X Genomics). Spatial transcriptomics assays were barcoded based on tissue-covered capture spot and library preparation was performed with 10X Genomics using dual-end indices. Paired end sequencing was performed on an Illumina Novaseq instrument. Low-level analysis, including demultiplexing, mapping to a reference transcriptome (mm10-2020-A or GRCh38-2020-A), and eliminating redundant UMIs, was performed with Cell Ranger 6.1.1 pipeline for 10X samples.