Unveiling 10x Genomics' Latest Innovations
From sample preparation through single-cell and spatial technology
In February, after the AGBT (Advances in Genome Biology and Technology) conference, I learned about the new products from 10x Genomics. Then, last month, at the 10x Genomics Single Cell & Spatial Discovery Symposium in Berlin, I had the chance to speak with researchers who got early access to those products. In this blog, I'll share what I discovered about the new things that are already available or coming soon.
Singe-cell approaches
1. Sample prep protocols > Whole blood fixation
10x Genomics has a new officially supported sample preparation protocol. It is to fix whole blood samples prior to the use of the Single Cell Gene Expression Flex kit (Flex). There will also be a new solution or solutions to preserve samples before using the Next GEM1 and GEM-X2 kits.
Honestly, I'm hoping this is true, because it will make experimental planning a lot easier and less stressful whenever we need these kits.
2. The kits
Next GEM > GEM-X
The Next GEM kits for gene expression (Single Cell Gene Expression 3’ v3.1, Single Cell Immune Profiling 5’v2) have new versions. They are called GEM-X kits: Single Cell Gene Expression v4 and Single Cell Immune Profiling v3. We can only use them on the Chromium X series instruments. What is the promise?
cell recovery rates of up to 80% (now 60–65%)
2-fold increase in cell throughput
2-fold reduction in multiplet rate
up to 2 times more detected genes
2-fold reduction in cost per cell
Will the 3’ and 5’ Next GEM kits be discontinued in the future? My guess is, yes.
Will 10x Genomics have 2 products for the same thing? Especially if one is a lot better than the other? I don’t think so.
If the GEM-X kits are so good as they are told, why should we use the Next GEM kits? Unless off course we need to finish a project that was already started.
Flex Assays > New information layers
Last year, 10x Genomics launched the Flex kit for fixed cells. This year, they plan to release new assays where we will be able to detect not only mRNA but also intracellular proteins or CRISPR guides.
3. The Chromium Platform
In 2017, 10x Genomics introduced the Chromium Controller. Then, in 2021, they released the Chromium X Series, which includes the Chromium iX and Chromium X. All can perform experiments for 10K cells. If we need more cells at once, Chromium X is our only choice.
As for kits, we can use the Next GEM kits on all platforms. However, the Flex and the GEM-X kits can only be used with the Chromium X Series instruments.
If you are thinking in getting a 10x Genomics instrument for single cell experiments, choose between the Chromium iX and Chromium X. The Chromium Controller was considered obsolete at the end of 2022 by 10x Genomics and the company has plans to discontinue it at the end of this year34. However, do not panic, and I will state: “We have established an inventory reserve for Chromium Controller instrument support through the end of 2027 (December 31, 2027) for instruments under warranty or covered by an active Assurance Plan. Warranty support for assays performed on Chromium Controller will be available until the end of 2028.”
Spatial Transcriptomics
1. Visium > Visium HD
The Visium Spatial Gene Expression Assays (Visium) let us study mRNA expression in tissues and track where each gene is. The first kit used polyA chemistry and was only for fresh-frozen tissue. Later, they introduced a probe-based kit that works with both fresh-frozen and Formalin-Fixed Paraffin Embedded Tissues (FFPE) tissues. The last kits came with a companion instrument called Visium CytAssist, making experiments smoother. The biggest limitation is the lack of single cell resolution.
To solve this, 10x Genomics developed the Visium HD, already launched for FFPE tissues. Note: The use of Visium CytAssist is mandatory here.
2. Xenium > More probes, Cell segmentation and RNA & Proteins
The Xenium spatial platform is being used by different labs. This assay is compatible with fresh, frozen and FFPE tissue and for now, allows the use of between 100 and 1K probes. The company plans to increase this to 5K genes per panel this year.
One challenge, common in spatial transcriptomics is cell segmentation—figuring out where one cell begins and ends. This can be tricky with irregular-shaped cells like neurons.
To tackle this, 10x Genomics created an add-on kit paired with a smart algorithm (machine learning) to refine cell segmentation. It's called multimodal cell segmentation and is currently available for human and mouse samples. It uses different markers: DAPI, different protein antibodies, and 1 RNA probe.
Additionally, later this year, they're rolling out a multiplex protein profiling solution. It'll allow us to analyze mRNA expression and protein levels in the same tissue section in one go.
This are all the updates that I have for now. If you are interested in learning about real life experiments performed by early access users, read this other blog post.
Thank you for reading ❤️.
Single Cell Gene Expression 3’ v3.1, Single Cell Immune Profiling 5’v2, Single Cell ATACseq, and Single Cell Multiome
Single Cell Gene Expression 3’ v4, Single Cell Immune Profiling 5’v3
https://www.10xgenomics.com/instruments/chromium-controller
https://www.genomeweb.com/business-news/10x-genomics-discontinue-legacy-chromium-controller-favor-x-series