Visium Direct Mount Fresh Frozen -- University of Minnesota TMCs
Laura J Niedernhofer, David A Bernlohr
Abstract
The Visium Spatial Gene Expression Solution measures the total mRNA in tissue sections and requires a Visium Spatial slide with intact tissue sections as input. This protocol outlines methanol fixation, Hematoxylin & Eosin (H&E) staining, and imaging of tissue for use with 10x Genomics Visium Spatial protocols. Fixed and stained tissue sections are inputs for the downstream Visium Spatial Tissue Optimization and Visium Spatial Gene Expression workflows.
Tissue sections are processed with Visium Spatial Gene Expression assay performed by the University of Minnesota Imaging Center and sequenced by the University of Minnesota Genomics Center.
Steps
Tissue Optimization
CG000238 Rev E 10x FF Visium Spatial Tissue Optimization.pdf
Fixation, H&E Staining & Imaging
CG000160 Rev C 10x FF Visium Methanol Fixation and HE Staining.pdf
Library Preparation & Sequencing
CG000239 RevF 10x FF Visium Spatial Gene Expression User Guide.pdf
FASTQ Generation
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0
