• BaseSpace™ Sequence Hub
  • News
  • 05/31/2022

10x Genomics Chromium 3’ Gene Expression (Dual Index) data now available on Illumina® BaseSpace™ Sequence Hub

Author:
  • 20638862 135027957099699 8813390929948020528 n
    Sophie Wehrkamp-Richter

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

Single-cell RNA-sequencing is a next-generation sequencing (NGS) method that examines the transcriptomes of indi­vidual cells, providing a high-resolution view of cell-to-cell variation. 10x Genomics is a partner that develops multiple single cell and spatial biology solutions. The Chromium Single Cell Gene Expression assay provides single cell transcriptome 3' gene expression and multiomic capabilities.

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 P2 flow cell, and another set of libraries sequenced on a NovaSeq™ 6000 SP v1.5 flow cell.

10x Genomics Chromium Single Cell Gene Expression workflow

A typical single cell RNA-Seq experiment with 10x Genomics Chromium Single Cell Gene Expression starts with a single cell or single nuclei suspension, followed by library preparation on the Chromium instrument (figure 1 below).

Figure 1: The overall workflow for preparing 10x Genomics Single Cell Gene Expression libraries starts with a single cell or single nuclei suspension, followed by microfluidic single cell partitioning and barcoding with the Chromium instrument. Sequencing for the single-cell gene expression library then happens on Illumina® instruments, followed by analysis and data visualization using 10x Genomics Cell Ranger and Loupe Browser software. Single-cell sequencing data can also be analyzed using the Illumina DRAGEN™ Single-Cell app, available in the cloud on BaseSpace™ Sequence Hub, or locally on the NextSeq 1000 and NextSeq 2000 instruments.

The 10x Genomics Chromium Single Cell Gene Expression assay is compatible with all Illumina® platforms, but we recommend using NextSeq™ 550/1000/2000 and NovaSeq™ 6000 to be able to sequence multiple samples per run (see table 1 below).


10x Genomics Chromium Single Cell Gene Expression runs available on BSSH demo data page

To view a set of sequencing runs for 10x Genomics Chromium Single Cell 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 published run data.

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

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


NovaSeq™ 6000 SP v1.5 flow cells:

Link to run: https://basespace.illumina.com/s/sOoqekCqOk6x

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

NextSeq™ 2000 P3 flowcell

Link to run: https://basespace.illumina.com/s/UQEhwKFoCvj8

Link to project: https://basespace.illumina.com/s/Q7CVCBgSpp0i


Access the 10x Genomics Cell Ranger html report for the Chromium Single Cell Gene Expression dataset

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

The Cell Ranger summary report contains summary metrics and automated secondary analysis results. The number of cells detected, mean reads per cell, and median genes per cell are prominently displayed near the top of the page. The analysis tab contains additional information such as a t-SNE projection.



Additional resources

If you need further assistance in sequencing 10x Chromium Single Cell Gene Expression libraries, you can contact the Illumina® (techsupport@illumina.com) and 10x Genomics (support@10xgenomics.com) support teams. These 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 generating and sequencing 3’ Chromium GEX libraries on their NovaSeq and NextSeq 2000 instruments.