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  • 08/07/2023

10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression data on NovaSeq™ X series now available on BaseSpace™ Sequence Hub

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    Sophie Wehrkamp-Richter

Today, we’re thrilled to share NovaSeq X series data for single cell analysis in collaboration with 10x Genomics, a partner that develops multiple single cell and spatial biology in situ solutions.

Single-cell analysis can help tease apart heterogeneity in complex cell populations, distinguishing cell types and revealing dynamic cell states. The 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression prepares sequencing-ready libraries to simultaneously profile gene expression and chromatin accessibility from the same cell.

Today, we are excited to announce that we have published NovaSeq X sequencing data for this product on BaseSpace Sequence Hub.

10x Genomics Multiome assay workflow

The 10x Genomics Multiome assay distinguishes itself from other experimental designs that combine multiple “omes” by using the single-cell barcodes to directly link chromatin accessibility data to gene expression data. This is achieved by generating both ATAC and 3' gene expression libraries from the same starting material.

Figure 1: The overall workflow for preparing 10x Genomics Multiome libraries starts with a nuclei suspension, followed by microfluidic single-cell partitioning and barcoding with a compatible Chromium instrument. Sequencing for the two resulting Multiome libraries (one single-cell ATAC-Seq library and one single-cell gene expression library) then happens on Illumina® instruments, followed by analysis and data visualization using 10x Genomics Cell Ranger ARC and Loupe Browser software.

The 10x Genomics Multiome assay is compatible with all Illumina® platforms, but we recommend sequencing on NovaSeq X series/ NovaSeq 6000 and NextSeq 1000/2000 to enable sequencing multiple samples per run (see table below). Due to differences in read configuration and recommended sequencing depths, Multiome gene expression libraries should be run on separate flow cells from Multiome ATAC libraries.

Table 1: example sample throughput for Chromium Single Cell Multiome assay on Illumina sequencing systems

❶ Minimum read recommendations, courtesy of 10x Genomics

❷ Adjust sequencing depth for the required performance of application. The sequencing saturation metric and curve in the Cell Ranger ARC summary can be used to optimize sequencing depth for specific sample types.

❸ 50K individual reads; 25K from Read 1 and 25K from Read 2

❹ P2 flowcells with the same samples throughput are also available on the NextSeq 1000 System

❺ this throughput requires individual lane loading

10x Genomics Multiome runs available on BSSH demo data page

To view a set of sequencing runs for 10x Genomics Multiome libraries run on NovaSeq X series, please visit BaseSpace Sequence Hub. Check our previous blogpost to access NovaSeq 6000 and NextSeq 2000 sequencing runs with 10x Genomics Multiome libraries.

Check blog post Demo Data Page" for additional details on how to access the run data on the demo data page.

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

You can use the demo data run to compare with your own 10x Genomics Multiome runs. Check the blog post Does my sequencing run look goodfor additional details on how to estimate sequencing your run quality.

NovaSeq X (10B): 10x Genomics Multiome ATAC + Gene Expression

Sequencing was performed on the NovaSeq X Plus System with NovaSeq X Series 10B Reagent Kit (300 cycles). The loading concentration for each run was 175 pM and 1% of the positive control PhiX was spiked in.

10 libraries were loaded per flowcell lane for a total of 80 replicates in one run. A sample sheet showing the indexes for each sample is available for each run.

Multiome GEX run: https://ilmn-sso.basespace.illumina.com/s/n41YxIxsgkba

Multiome ATAC run: https://ilmn-sso.basespace.illumina.com/s/YgvdxLjDJaSt

Multiome project: https://ilmn-sso.basespace.illumina.com/s/XkXrLjalsBog

Access the 10x Genomics Cell Ranger ARC html report for the Multiome dataset

The html run reports from Cell Ranger ARC have been uploaded to the project, under the “Analyses” tab. 3 samples were provided by 10x Genomics and have been sequenced on these runs. The HTML report files generated by Cell Ranger ARC have been included in the project folder and can be downloaded from the “Files” tab.

The summary report contains summary metrics and automated secondary analysis results. The number of cells detected, ATAC median high-quality fragments per cell, and GEX median genes per cell are prominently displayed near the top of the page.

Additional resources

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

Additional resources and dataset examples are available here:

Special thanks to our colleagues at 10x Genomics for providing samples to sequence. Hat tip to System Integration Kevin Thai for sequencing and analyzing these runs for this collaboration, and Bioinformatics Manager Steve Lee for publishing them on BaseSpace.

For Research Use Only. Not for use in diagnostic procedures. M-GL-01955