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10X Visium data

JZ Jiaqiang Zhu
SS Shiquan Sun
XZ Xiang Zhou
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The 10X Visium is a platform that builds upon on the original Spatial Transcriptomics technology with improvements on both resolution (55-micron resolution, with smaller distance between barcoded regions) and experimental time. We obtained a Visium dataset collected on the human heart tissue from the 10X Visium spatial gene-expression repository (https://support.10xgenomics.com/spatial-gene-expression/datasets/1.1.0/V1_Human_Heart). The data contains 36,601 genes measured on 4247 spots with known spatial location information. Each spot is a 55-micron well. We filtered out mitochondrial genes and genes that are not expressed in any spot. We analyzed a final set of 20,904 genes on 4247 spots. The 10X Visium human heart data is relatively sparse with 90.81% of entries being 0 (Additional file 1: Table S1). In addition, we also obtained a Visium dataset collected on the human ovarian cancer tissue from the 10X Visium spatial gene-expression repository (https://support.10xgenomics.com/spatial-gene-expression/datasets/1.2.0/Targeted_Visium_Human_OvarianCancer_Pan_Cancer). The data contains 1198 genes measured on the 3493 spots. After removing spot with no gene-expression count, we analyzed a final set of 1198 genes on 3492 spots. Since this data is generated with an enriched library prepared using the Human Pan-Cancer Panel, only 73.78% of entries are 0.

Copyright and License information: The Author(s) ©2021
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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