Size matters - the impact of nucleus size on results from spatial transcriptomics

Mohammadi, E.; Chojnowska, K.; Bienkowski, M.; Kostecka, A.; Koczkowska, M.; Zmijewski, M. A.; Jakalski, M.; Ingelsson, M.; Filipowicz, N.; Olszewski, P.; Davies, H.; Wierzbicka, J. M.; Hyman, B. T.; Dumanski, J. P.; Piotrowski, A.; Mieczkowski, J.

doi:10.1101/2022.03.31.486657

bioRxiv · 10.1101/2022.03.31.486657

Size matters - the impact of nucleus size on results from spatial transcriptomics

Mohammadi, E.·Chojnowska, K.·Bienkowski, M.·Kostecka, A.·Koczkowska, M.·Zmijewski, M. A.·Jakalski, M.·Ingelsson, M.·Filipowicz, N.·Olszewski, P.·Davies, H.·Wierzbicka, J. M.·Hyman, B. T.·Dumanski, J. P.·Piotrowski, A.·Mieczkowski, J.

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Abstract

Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover novel modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei. Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on results from spatial transcriptomic study of human postmortem brains. CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain.

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Mohammadi, E., Chojnowska, K., Bienkowski, M., Kostecka, A., Koczkowska, M., Zmijewski, M. A., Jakalski, M., Ingelsson, M., Filipowicz, N., Olszewski, P., Davies, H., Wierzbicka, J. M., Hyman, B. T., Dumanski, J. P., Piotrowski, A., Mieczkowski, J.. 2022-04-01. Size matters - the impact of nucleus size on results from spatial transcriptomics. https://doi.org/10.1101/2022.03.31.486657

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