Mar 12, 2024

Public workspaceVisium Direct Mount FFPE v3 -- University of Minnesota TMCs V.3

DOI
https://dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v3
  • Laura J Niedernhofer1,
  • David A Bernlohr1
  • 1University of Minnesota, Minneapolis, MN
  • Cellular Senescence Network (SenNet) Method Development Community
Allie Abdellatif
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DOI: https://dx.doi.org/10.17504/protocols.io.kxygx3qpkg8j/v3
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 Abdellatif
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
Keywords: visium spatial gene expression for ffpe, visium spatial gene expression, visium direct mount ffpe v3, visium spatial slide with intact tissue section, mrna in tissue section, gene expression, tissue sample, university of minnesota genomics center, tissue section, visium spatial slide, minnesota genomics center, mrna, ffpe, intact tissue section, university of minnesota imaging center
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.


Troubleshooting
Deparaffinization, H&E Staining, Imaging & Decrosslinking
Download CG000409_Demonstrated_Protocol_VisiumSpatialFFPE_Deparaffin_H_E_RevD.pdfCG000409_Demonstrated_Protocol_VisiumSpatialFFPE_Deparaffin_H_E_RevD.pdf3.1MB

Library Preparation & Sequencing
Download CG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevE.pdfCG000407_VisiumSpatialGeneExpressionforFFPE_UserGuide_RevE.pdf6.3MB
Note
Sequencer: Illumina NovaSeq 6000 using read format 28/10/10/50



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