Dec 19, 2023

Public workspaceVisium Direct Mount Fresh Frozen -- University of Minnesota TMCs

DOI
dx.doi.org/10.17504/protocols.io.6qpvr3qdovmk/v1
  • Laura J Niedernhofer1,
  • David A Bernlohr1
  • 1University of Minnesota, Minneapolis, MN
Allie Pybas
Open access
DOI: dx.doi.org/10.17504/protocols.io.6qpvr3qdovmk/v1
Protocol Citation: Laura J Niedernhofer, David A Bernlohr 2023. Visium Direct Mount Fresh Frozen -- University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.6qpvr3qdovmk/v1
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: November 30, 2023
Last Modified: December 19, 2023
Protocol Integer ID: 91658
Funders Acknowledgement:
NIH
Grant ID: 5U54AG079754-02
NIH
Grant ID: 5U54AG076041-03
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.
Tissue Optimization
Tissue Optimization
Download CG000238 Rev E 10x FF Visium Spatial Tissue Optimization.pdfCG000238 Rev E 10x FF Visium Spatial Tissue Optimization.pdf4.4MB

Fixation, H&E Staining & Imaging
Fixation, H&E Staining & Imaging
Download CG000160 Rev C 10x FF Visium Methanol Fixation and HE Staining.pdfCG000160 Rev C 10x FF Visium Methanol Fixation and HE Staining.pdf1.2MB

Library Preparation & Sequencing
Library Preparation & Sequencing
Download CG000239 RevF 10x FF Visium Spatial Gene Expression User Guide.pdfCG000239 RevF 10x FF Visium Spatial Gene Expression User Guide.pdf6.6MB

Note
Illumina NovaSeq 6000 with read format 28/10/10/90

FASTQ Generation
FASTQ Generation
BCL data from Illumina sequencer is demultiplexed and converted into FASTQ format using bcl2fastq version 2.20.0