Dec 20, 2023

Public workspaceVisium CytAssist FFPE v4 -- University of Minnesota TMCs V.4

DOI
https://dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v4
  • 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.n92ldmn99l5b/v4
Protocol Citation: Laura J Niedernhofer, David A Bernlohr 2023. Visium CytAssist FFPE v4 -- University of Minnesota TMCs. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ldmn99l5b/v4Version 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: December 20, 2023
Last Modified: December 20, 2023
Protocol Integer ID: 92580
Keywords: visium cytassist spatial gene expression for ffpe assay, visium cytassist spatial gene expression, visium spatial gene expression, visium cytassist ffpe v4, mrna in tissue section, gene expression, ffpe assay, tissue sample, visium cytassist instrument, university of minnesota genomics center, minnesota genomics center, mrna, ffpe, tissue section
Funders Acknowledgements:
NIH
Grant ID: 5U54AG079754-02
NIH
Grant ID: 5U54AG076041-03
Abstract
The Visium CytAssist Spatial Gene Expression for FFPE assay is designed to analyze mRNA in
tissue sections derived from formalin fixed & paraffin embedded (FFPE) tissue samples. The Visium
CytAssist instrument requires a glass 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 CG000520_Demonstrated_Protocol_VisiumCytAssist_Deparaffin_H_E_RevB.pdfCG000520_Demonstrated_Protocol_VisiumCytAssist_Deparaffin_H_E_RevB.pdf3.1MB

Library Preparation & Sequencing
Download CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevD.pdfCG000495_VisiumCytAssist_GeneExpressionUserGuide_RevD.pdf31.3MB

Note
Illumina NovaSeq 6000 with 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