Spatial transcriptome analysis

Question

[siu]

Hi, I have two samples of Spatial transcriptome (Visium), one for wild type and one for knock out that I have analyzed using SpaceRanger count (I am new in this type of analysis).I need to compare the annotated UMAP plot of wild type and knock out samples. I am following the Seurat tutorial for doing the downstream analysis:

https://satijalab.org/seurat/articles/spatial_vignette.html

But I am not getting, how can I compare these (by making two separate seurat objects and then merging them) and doing this type of analysis

"https://satijalab.org/seurat/articles/integration_introduction.html" ?

Also, how can I annotate the UMAP clusters? I Know, I can use FindMarkers to find the maker genes in every cluster but I don't know what I will do after this.

Please help

Thanks in Advance

[Omics data mining]

Hello

For spatial transcriptome analysis, there are a couple of ways you can go about it.

1. If you're looking to analyze individual samples (both ct and knock out separately) , you can use either Seurat R or squidpy python packages. However, if you're interested in comparing data, integrating both datasets may be the way to go. There are many ways to do this, with one helpful link being https://satijalab.org/seurat/articles/spatial_vignette.html.

2. If you have single cell data for your samples, performing convolution can help you identify enriched cell types and annotate your umap accordingly.

[siu]

Thank you so much for your insight.

I have another question regarding the quality filtering of the spots. In the tutorial that you had mentioned, there is no quality filtering of spots. However, I saw some tutorial which do the spot cleaning. Is there any recommended cut off to remove the low quality spot? When I am applying their cut off, most of the spots were filtered out and when I am not doing the spot cleaning, the UMAP clustering is not good.