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Distribution of Transcripts per Cell in Spatial Transcriptomics (Xenium)

Hi all,

I am working on a Spatial Transcriptomics dataset generated with Xenium.

I have the following distribution of Transcripts per cell:

enter image description here

However when I compare to the SpatialData tutorial for Xenium where they got the following distribution:

enter image description here

I see that they have lots of cells with low number of transcripts, while I have not a skewed distribution but rather most cells with a significant number of transcripts. I wonder which conclusion I can draw. I would say this is a rather positive observation but I would appreciate any insight.

Thank you very much

xenium spatial-transcriptomics spatialdata spatial-omics
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updated by Bastien Hervé Bastien Hervé • written by npont • npont

We would need more information about the gene panel and the segmentation strategy used and the type of tissue.

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written by Bastien Hervé Bastien Hervé

We used a custom gene panel of 100 genes for Xenium. This panel includes markers of different differentiation stages of neural stem cells. Concerning the type of segmentation, it is the multi-modal segmentation of Xenium which is based on nucleus, membrane and interior RNA staining. We are looking the telencephalon, a specific structure of the brain rich in neural stem cells.

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written by npont • npont

Thanks ! And about the SpatialData ? If your cells are all stem cells, they have a comparable transcriptome, thus it makes sense that they all have more or less the same number of transcriptional information.

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written by Bastien Hervé Bastien Hervé

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