Introduction to spatialLIBD

Leonardo Collado-Torres1,2*, Kristen R. Maynard1** and Andrew E. Jaffe1***

1Lieber Institute for Brain Development, Johns Hopkins Medical Campus
2Center for Computational Biology, Johns Hopkins University

*lcolladotor@gmail.com
**Kristen.Maynard@libd.org
***andrew.jaffe@libd.org

Package

spatialLIBD 1.17.8

Contents

1 Welcome

Welcome to the spatialLIBD project! It is composed of:

• a shiny web application that we are hosting at spatial.libd.org/spatialLIBD/ that can handle a limited set of concurrent users,
• a Bioconductor package at bioconductor.org/packages/spatialLIBD (or from here) that lets you analyze the data and run a local version of our web application (with our data or yours),
• and a research article with the scientific knowledge we drew from this dataset. The analysis code for our project is available here and the high quality figures for the manuscript are available through Figshare.

The web application allows you to browse the LIBD human dorsolateral pre-frontal cortex (DLPFC) spatial transcriptomics data generated with the 10x Genomics Visium platform. Through the R/Bioconductor package you can also download the data as well as visualize your own datasets using this web application. Please check the manuscript or bioRxiv pre-print for more details about this project.

If you tweet about this website, the data or the R package please use the #spatialLIBD hashtag. You can find previous tweets that way as shown here. Thank you!

1.1 Study design

As a quick overview, the data presented here is from portion of the DLPFC that spans six neuronal layers plus white matter (A) for a total of three subjects with two pairs of spatially adjacent replicates (B). Each dissection of DLPFC was designed to span all six layers plus white matter (C). Using this web application you can explore the expression of known genes such as SNAP25 (D, a neuronal gene), MOBP (E, an oligodendrocyte gene), and known layer markers from mouse studies such as PCP4 (F, a known layer 5 marker gene).