• BaseSpace™ Sequence Hub
  • News
  • 07/30/2021

10x Genomics Visium Spatial Gene Expression data now available on Illumina® BaseSpace™ Sequence Hub

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    Sophie Wehrkamp-Richter

Today, we’re sharing the fourth in a series of posts that shed more light on new run data publicly available on BaseSpace Sequence Hub (BSSH).

Spatial transcriptomics experiments combine molecular and morphological characterization to provide a previously inaccessible view of tissue biology. 10x Genomics is a partner that develops multiple single cell and spatial biology solutions. The 10x Genomics Visium Spatial Gene Expression maps the whole transcriptome with morphological context in FFPE and fresh-frozen tissues.

Today, we are excited to announce that we have published sequencing data for this product on BaseSpace™ Sequence Hub, including one set of libraries sequenced on the NextSeq™ 2000 P3 flow cell, and another set of libraries sequenced on a NovaSeq™ 6000 SP v1.5 flow cell.

10x Genomics Visium Spatial Gene Expression workflow

A typical spatial RNA-Seq experiment with 10x Genomics Visium Spatial Gene Expression follows a workflow of tissue sample preparation, imaging, library prep, sequencing, and analysis. The 10x Genomics Visium Spatial Gene Expression assay is compatible with all Illumina® platforms, but we recommend sequencing on NextSeq™ 550/1000/2000 and NovaSeq™ 6000 to be able to sequence multiple samples per run (see table 1 below).

Figure 1: Workflow for a spatial RNA-Seq experiment—Section fresh frozen or FFPE tissue onto a Visium Spatial Gene Expression slide, then stain and image the tissue sections. The glass slide captures mRNA with barcoded oligonucleotide probes and cDNA synthesis is followed by library construction. Sequence whole-transcriptome gene expression libraries on Illumina instruments. Gene expression location is connected with the tissue morphology using Space Ranger and Loupe Browser software from 10x Genomics.

10x Genomics Visium Spatial Gene Expression runs available on BSSH demo data page

To view a set of sequencing runs for 10x Genomics Visium Spatial Gene Expression libraries run on both NextSeq™ 2000 P3 flow cells and NovaSeq™ 6000 SP v1.5 flow cells, please visit BaseSpace™ Sequence Hub. Check our previous blog post on our Demo Data section in BaseSpace™ Sequence Hub for additional details on how to access the run data on the demo data page.

Below are two links to directly import the runs and project folders into your BaseSpace account. These runs can be found under the category “RNA-seq”. Because these are public data sets, these data sets are free and do not count against storage limits.

You can use the demo data to compare with your own 10x Genomics Visium Spatial Gene Expression runs. See our first blog post in this series on evaluating sequencing runs for additional details on how to estimate sequencing your run quality.

NovaSeq 6000 SP v1.5 flow cells:

Link to run: https://basespace.illumina.com/s/WHTkHhVLBsan

Link to project: https://basespace.illumina.com/s/4lQYhLKiV2Ou

NextSeq™ 2000 P3 flowcell

Link to run: https://basespace.illumina.com/s/rzwY81CM9EC5

Link to project: https://basespace.illumina.com/s/AzdUKMkqgrCu

Access the 10x Genomics Space Ranger ARC html report for the Visium Spatial Gene Expression dataset

The html run reports from Space Ranger ARC have been uploaded to the project, under the “Analyses” tab. 8 samples were provided by 10x Genomics and have been sequenced on these runs. The HTML report files generated by 10x Space Ranger ARC have been included in the project folder and can be downloaded from the “Files” tab (under the “Report html” folder).

The summary report contains summary metrics and automated secondary analysis results. Number of spots under tissue, mean reads per spot and median genes per spots are prominently displayed near the top of the page.

Additional resources

If you need further assistance in sequencing 10x Visium Spatial Gene Expression libraries, you can contact the Illumina® (techsupport@illumina.com) and 10x Genomics (support@10xgenomics.com) support teams. The two teams collaborate to ensure you are fully supported throughout the workflow.

Additional resources and dataset examples are available here:

Products mentioned here are for research use only, and are not for diagnostic use.

Special thanks to our colleagues at 10x Genomics for providing samples to sequence, and hat tip to Illumina Scientist Robin Bombardi and the Emerging Apps team for sequencing and analyzing these runs for this collaboration.