GSM7843145: Head_E15.5_WT_rep1; Mus musculus; RNA-Seq
Tissues were prepared as formalin-fixed paraffin-embedded (FFPE) tissue sections, following the 10X Genomics Visium Manual Workflow for FFPE. All steps from 10X Genomics' FFPE Visium Spatial workflow were followed. In brief, spatial RNA sequencing (spRNA-seq) slides are coated with an array of poly-T primers, which encode unique spatial barcodes. These barcodes contain thousands of encoded oligonucleotides within a catchment frame of 6.5 × 6.5 mm. The oligonucleotides are selectively hybridized with the 3' end of mRNA eluted upon tissue permeabilization, enabling scRNA-seq-like mRNA sequencing with the individual barcode spots replacing the individual suspended cells. Each barcoded spot on the slide is ~55 µm in diameter, which is predicted to capture ~10 cells per spot. FFPE tissue was sectioned directly onto the barcoded slide, H&E stained, and then underwent enzymatic permeabilization, which allowed for mRNA release and subsequent capture by primer-coated slides. These mRNA molecules are visualized through the incorporation of fluorescent nucleotides into the complementary DNA (cDNA) synthesis process. Spatial Transcriptomics