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Xenium_Samui_readme.md

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This is the Samui browser for adult human hypothalamus (VMH/ARC) Xenium data from Mulvey, et. al. If you're looking for the Visium browser, please go here.

Information to match sample IDs as listed in browser to those in the manuscript are in a table at the end of this document.

Using the dropdown menu at the top of this sidebar, you can choose to visualize cell-level log-normalized gene expression, clustering results and domain (VMH/ARC/other) assignments, and QC metrics. You can then use the adjacent text entry field to filter the selected feature (choices will appear if you place your text cursor here). The different choices in the dropdown menu are:

  • Banksy-Cluster: The 33 cluster labels retained after removing sample/donor-specific clusters.
  • Banksy Cluster Group: Clusters from above aggregated into broader cell types (e.g., astrocyte clusters all under one "astrocyte" label)
  • Domain of Cell: The VMH/ARC/other assignment for each cell determined using k nearest-neighbors smoothing as described in the manuscript
  • nCounts: total number of gene counts for each cell
  • nGenes: total number of unique genes detected in each cell
  • Cell Area: area of each xeniumranger 1.7-segmented cell
  • Nucleus Area: area of each xenium ranger 1.7-segmented nucleus

Visualizing two features/annotations simultaneously:

To visualize two separate features at once (one as outlines and the other as fill for each point (cell)), click the "Add Layer" button in the top right of the viewer interface, then choose a second feature. In the list of shown features, the left checkbox toggles whether a feature and filter is displayed as the outline of each point, and the right checkbox will toggle whether that feature and filter is displayed as the fill for each point.

Additional resources of note:

Samui ID Manuscript ID Sex Donor
X99_1225A x1225B_M Male Br1225
X99_1225B x1225C_M Male Br1225
X97_reg1 x1735B_M Male Br1735
X97_reg2 x1735C_M Male Br1735
X36_5459A x5459B_M Male Br5459
X36_5459B x5459C_M Male Br5459
X86_reg2 x5993B_F Female Br5993
X86_reg3 x5993C_F Female Br5993
X86_reg1 x6197B_M Male Br6197
X97_reg3 x6588C_F Female Br6588
X36_8667C x8667B_F Female Br8667
X99_8741C x8741C_F Female Br8741
X99_8741D x8741D_F Female Br8741