Jan 26, 2023

Public workspaceSpatial Transcriptomics for OCT using 10x Genomics Visium

DOI
dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1
  • 1Department of Medicine, Washington University in St Louis
Andrew Houston
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DOI: dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/v1
Protocol Citation: Andrew Houston, Siqi Chen, Feng Chen 2023. Spatial Transcriptomics for OCT using 10x Genomics Visium. protocols.io https://dx.doi.org/10.17504/protocols.io.x54v9d3opg3e/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: January 24, 2023
Last Modified: January 26, 2023
Protocol Integer ID: 75822
Abstract
To detect gene expression spatially mapped across a fresh-frozen tissue sample adapted from 10x Genomics Visium protocol.
Visium Fresh-Frozen
Visium Fresh-Frozen
Start here
If performing OCT tissue embedding for the first time be sure to consult pgs.5-9
If utilizing a new tissue type for the first time be sure to utilize the Tissue Optimization Guide which can be found here
RNA extraction and assessment is outlined in the above guide but not always necessary
Most OCT blocks have preserved RNA quality well due to their preservation/storage
Perform all fixation/H&E staining/imaging steps on the Visium Spatial Gene Expression Slide (PN-2000233)
Utilize the guide here
Typically it is not necessary to utilize a coverslip while imaging

Immediately proceed to the Visium Library Construction
Start on pg. 35 using this guide here
Sequence the libraries according to the requirements on pg. 59 of CG000239