• BaseSpace™ Sequence Hub
  • News
  • 03/20/2023

10x Genomics’ Chromium Single Cell Gene Expression Flex data now available on Illumina® BaseSpace™ Sequence Hub

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    Sophie Wehrkamp-Richter

Today, we’re continuing a series of posts that shed more light on new run data publicly available on BaseSpace Sequence Hub (BSSH) for applications like single cell.

Single cell RNA-sequencing is a next-generation sequencing (NGS) method that examines the transcriptomes of individual cells, providing a high-resolution view of cellular heterogeneity. 10x Genomics is a partner that develops multiple single cell and spatial biology solutions. Chromium Single Cell Gene Expression Flex assay from 10x Genomics enables gene expression profiling for thousands to hundreds of thousands of cells or nuclei with a sensitive probe-based method that captures the whole human or mouse transcriptome to detect even low-expressing genes. This assay is compatible with fresh, PFA-fixed, and FFPE samples.

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.

Figure 1 - Chromium Single Cell Gene Expression Flex enables an efficient and streamlined workflow for sample management and processing. Samples are fixed and permeabilized and can be safely stored or transported without compromising data quality. Once ready to proceed, samples are hybridized to probe sets and may be processed individually (singleplex workflow) or pooled with up to 16 samples in a single lane of a Chromium chip (multiplex workflow). During GEM generation, the probe sets are ligated and extended to incorporate unique barcodes. Sequencing libraries are then prepared, sequenced on Illumina high throughput platforms, and analyzed using Cell Ranger and Loupe Browser software tools from 10x Genomics.

The Chromium Single Cell Gene Expression Flex assay from 10x Genomics is compatible with all Illumina® platforms, but we recommend using NextSeq™ 550/1000/2000 and NovaSeq™ 6000/X to be able to sequence multiple samples per run. The recommended sequencing depth is a minimum 10,000 read pairs/cell. Sequencing depth can be adjusted based on the required performance and application. The recommended read length is 28 bp for Read 1, 10 bp for Index 1 (i7) and Index 2 (i5) and at least 90 bp for Read 2 (reverse read).

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

To view a set of sequencing runs for Chromium Single Cell Gene Expression Flex 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 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.

NextSeq2000 run: https://basespace.illumina.com/s/Sp98smv7yYdA

NextSeq2000 project: https://basespace.illumina.com/s/ter7n3LI5Lh6

NovaSeq6000 run: https://basespace.illumina.com/s/lq8s4pNN3uqn

NovaSeq6000 Project: https://basespace.illumina.com/s/l1fNduSHJA8y

Access the 10x Genomics Cell Ranger html report for the Chromium Single cell Gene expression flex

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.






Joint 10x Genomics – Illumina application note:





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.

For Research Use Only. Not for use in diagnostic procedures. M-GL-01655