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For remote attendees: Data downloads

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Ryan Mulqueen edited this page May 23, 2026 · 5 revisions

Data to be used in each workshop is listed below for download.

Note that paths will depend on your system, so initial data loading code blocks in each workshop need to be modified.

1. scRNA: Processing Basics Data download

input_dir <- "/data/shared/scRNA/GSM7500435_hbca_c126_filtered_feature_bc_matrix.h5"

2. scDNA: CopyKit

Downloadable data set (sample_obj.rds) from dropbox here.

3. scRNA Copy Number Inference

Downloadable data set (input_seu.rds) from dropbox here.

4. scRNA Integration

folders BCHBCA81R_10xfix and BCMHBCA81R_intron can both be downloaded from dropbox here.

Make sure to unzip the dropbox download before starting.

5. Spatial RNA Visium HD

In this tutorial, we will use one of 10X public datasets, Human Breast Cancer (Fresh Frozen).

More different tissue type data can be found at here

To download in bash (terminal environment).

Human breast version of workshop

# standard spaceranger output for visiumHD
# human breast
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_web_summary.html
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_cloupe_008um.cloupe
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_feature_slice.h5
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_metrics_summary.csv
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_molecule_info.h5
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_spatial.tar.gz
curl -O https://s3-us-west-2.amazonaws.com/10x.files/samples/spatial-exp/3.1.2/Visium_HD_FF_Human_Breast_Cancer/Visium_HD_FF_Human_Breast_Cancer_binned_outputs.tar.gz
## unzip
tar -xvf Visium_HD_FF_Human_Breast_Cancer_spatial.tar.gz
tar -xvf Visium_HD_FF_Human_Breast_Cancer_binned_outputs.tar.gz

and unzip

tar -xvf Visium_HD_FF_Human_Breast_Cancer_spatial.tar.gz
tar -xvf Visium_HD_FF_Human_Breast_Cancer_binned_outputs.tar.gz

Mouse brain version

# standard spaceranger output for visiumHD
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_web_summary.html
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_cloupe_008um.cloupe
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_feature_slice.h5
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_metrics_summary.csv
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_molecule_info.h5
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_spatial.tar.gz
curl -O https://cf.10xgenomics.com/samples/spatial-exp/3.0.0/Visium_HD_Mouse_Brain/Visium_HD_Mouse_Brain_binned_outputs.tar.gz
tar -xvf Visium_HD_Mouse_Brain_spatial.tar.gz
tar -xvf Visium_HD_Mouse_Brain_binned_outputs.tar.gz

6. Xenium (5k) in situ

The file is located here.

Note that this file is large (40GB) so unlikely to run well on a local setup. An HPC is most likely required.

# Download (~40 GB)
wget -c --progress=bar \
  -P RawData \
  https://s3-us-west-2.amazonaws.com/10x.files/samples/xenium/3.0.0/Xenium_Prime_Breast_Cancer_FFPE/Xenium_Prime_Breast_Cancer_FFPE_outs.zip

# Unzip
unzip RawData/Xenium_Prime_Breast_Cancer_FFPE_outs.zip \
  -d RawData/Xenium_Prime_outs/

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