Mar 12, 2024
Version 3
Visium Direct Mount FFPE v3 -- University of Minnesota TMCs V.3
- Laura J Niedernhofer1,
- David A Bernlohr1
- 1University of Minnesota, Minneapolis, MN
- Cellular Senescence Network (SenNet) Method Development Community
Protocol Citation: Laura J Niedernhofer, David A Bernlohr 2024. Visium Direct Mount FFPE v3 -- University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v3Version created by Allie Pybas
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: March 12, 2024
Last Modified: March 12, 2024
Protocol Integer ID: 96579
Funders Acknowledgements:
NIH
Grant ID: 5U54AG076041-03
NIH
Grant ID: 5U54AG079754-02
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.
Deparaffinization, H&E Staining, Imaging & Decrosslinking
Deparaffinization, H&E Staining, Imaging & Decrosslinking
CG000409_Demonstrated_Protocol_VisiumSpatialFFPE_Deparaffin_H_E_RevD.pdf3.1MB Library Preparation & Sequencing
Library Preparation & Sequencing
CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevE.pdf6.3MB Note
Sequencer: Illumina NovaSeq 6000 using read format 28/10/10/50
FASTQ Generation
FASTQ Generation
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq software version 2.20.0