Dec 20, 2023
Version 4
Visium CytAssist FFPE v4 -- University of Minnesota TMCs V.4
- Laura J Niedernhofer1,
- David A Bernlohr1
- 1University of Minnesota, Minneapolis, MN
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 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: December 20, 2023
Last Modified: December 20, 2023
Protocol Integer ID: 92580
Funders Acknowledgement:
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.
Deparaffinization, H&E Staining, Imaging & Decrosslinking
Deparaffinization, H&E Staining, Imaging & Decrosslinking
CG000520_Demonstrated_Protocol_VisiumCytAssist_Deparaffin_H_E_RevB.pdf3.1MB Library Preparation & Sequencing
Library Preparation & Sequencing
CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevD.pdf31.3MB Note
Illumina NovaSeq 6000 with 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