Spatial transcriptomics from clinically non inflammed human lymph nodes
Spatial transcriptomics from clinically non inflammed human lymph nodes
After surgical excision torn tissues were collected sterile phosphate buffered saline on ice and processed within one hour of resection. Following the commercial brochure of Visium gene expression kits (10x Genomics, PN-1000184) the tissue blocks were cut into 10-μm sections using cryostat and mounted on Visium gene expression slides (10x Genomics, PN-1000188). Sections on Visium Gene Expression slides were first fixed with pre-cooled methanol for 30 minutes and stained with CD20, CD4, CD31 and aSMA and imaged with confocal microscopy to visualize the fiducial frames of capture areas and cell compartmentalization in different sections. The optimal permeabilization time for murine lymph node sections was 6 minutes evaluated by 10x Genomics Visium tissue optimization kit (10x Genomics, PN-1000193) for in situ hybridization and reverse transcription. cDNA libraries were generated using Visium spatial gene expression 3′ library construction kit (10x Genomics, PN-1000190).