Visium Direct Mount FFPE v2 -- University of Minnesota TMCs
Laura J Niedernhofer, David A Bernlohr
Published: 2023-12-21 DOI: 10.17504/protocols.io.kxygx3qpkg8j/v2
Abstract
The Visium Spatial Gene Expression for FFPE is designed to measure mRNA in tissue sections derived
from formalin fixed & paraffin embedded (FFPE) tissue samples and requires a Visium Spatial slide
with intact tissue sections as input.
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
Deparaffinization, H&E Staining, Imaging & Decrosslinking
Library Preparation & Sequencing
2. Sequencer: Illumina NovaSeq 6000 using read format 28/10/10/50
CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevD.pdf
Note
FASTQ Generation
3.
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0
