Note: You don’t need to manually download everything here - please follow the instructions from the setup page to run this workbook.

Mouse brain (demo Stereo-seq v1.3 data)

We will be exploring a demo mouse brain dataset made public by STOmics:

Although not required for this workshop, the raw data and additional demo datasets are available to download here.

SAW (Stereo-seq Analysis Workflow) v8.1 was run to generate several output files that we will explore. The processed data will not be available indefinitely, however later you will see how to regenerate it for yourself. (See the SAW page)

You can download the SAW report here.

# Download report

download_missing(url="https://filesender.aarnet.edu.au/download.php?token=bb9f59bb-441d-49bc-a0b5-8a05f6d5a2c0&files_ids=23522487", destfile="data/C04042E3.report.tar.gz")

A primary output of SAW v8.1 is visualization.tar.gz. We will be extracting this file and examining the contents.

Warning: Relatively large file (4.9GB)!

# Download visualization.tar.gz

download_missing(url="https://filesender.aarnet.edu.au/download.php?token=bb9f59bb-441d-49bc-a0b5-8a05f6d5a2c0&files_ids=23522484", destfile="data/visualization.tar.gz")

Mouse liver (published data)

For our later downstream analysis, we will be using the following anndata-compatible data file:
DY1_D0_stereo-seq.h5ad

Warning: Relatively large file (4.4GB)!

# Download LISTA data

download_missing(url="https://filesender.aarnet.edu.au/download.php?token=1beae7a9-436e-4915-9e01-4f24360140aa&files_ids=23496582", destfile="data/DY1_D0_stereo-seq.h5ad")

The above link is only temporarily available for this workshop, but the data will be available later on from CNGBdb.

This file is from LISTA: LIver Spatio-Temporal Atlas, in which Stereo-seq to profile mouse liver homeostasis and regeneration following partial hepatectomy over several time points. Our file is from day 0, the first time point following hepatectomy.

So that we don’t have to spend time converting it, we’ll load a premade RDS file:

# Download rds file

download_missing(url="https://filesender.aarnet.edu.au/download.php?token=07174a85-a97c-4f03-a175-2b6a0650d73c&files_ids=23535906", destfile="data/DY1_D0.rds")

Next steps

Once the data has downloaded, you’re ready to move on!