Datasets: Slide-seqV2

Lukas M. Weber

Leader(s)

Difficulty & duration

Tier 1 (dataset)

  • difficulty: intermediate
  • duration: 1-2 days

Tier 2 (workflow)

  • difficulty: advanced
  • duration: 1-2 weeks

Abstract

Our current aims are:

  • Finalize SpatialExperiment class structure by creating and testing example datasets from several technological platforms (to be collected in STdata package)
  • Adapt visualization functions for data from each platform (to be collected in ggspavis package)
  • Create a short analysis workflow using one of the example datasets from each platform

This will allow us to build an integrated Bioconductor-based infrastructure for analyzing spatially resolved transcriptomics data. Ultimately, this will all be showcased in our OSTA online book.

So far, we have mainly worked with data from the 10x Genomics Visium platform. The STdata package (under development) currently contains two example datasets from the Visium platform (human DLPFC and mouse coronal).

In this set of “Dataset” challenges, we will aim to select and prepare several additional datasets for demonstration and testing purposes.

Slide-seqV2 (Stickels et al. 2020) is a spot-based spatially resolved transcriptomics platform. This platform allows measuring very large numbers of spots, although at relatively low depth (low numbers of detected genes per spot). This provides us with a slightly different test case for our Bioconductor-based infrastructure.

Targets

This challenge consists of two tiers:

Tier 1 (dataset)

The Tier 1 challenge consists of:

  • selecting a suitable publicly accessible Slide-seqV2 dataset
  • formatting it into a SpatialExperiment object
  • creating a reproducible script to create the object from the raw data files, saving the object, and adding these to the STdata package

As a starting point, we can use the make-data.R scripts from the existing objects in the STdata package:

Tier 2 (workflow)

If there is interest and capacity, we could then continue with the Tier 2 challenge:

  • write a complete short analysis workflow, using the SpatialExperiment object created in the Tier 1 challenge
  • format the analysis workflow as an RMarkdown file, which could later be integrated into the workflow chapters of our OSTA online book