DNA Technologies Core April News

The lab now supports spatial transcriptomics studies with the 10X Genomics Visium chemistries.

Visium Spatial Transcriptomics and Multi-omics (sequencing based) - Our lab now supports spatial transcriptomics studies on the Visium and Visium HD platforms with the help of our 10XGenomics CytAssist instrument for fresh-frozen, fixed-frozen, and FFPE tissue sections.  We are open to supporting other platforms. Please contact our expert Hong Qiu (honqiu@ucdavis.edu).

Visium employs arrays of location-encoded oligonucleotides with poly-T stretches to capture transcripts or probe constructs. This enables two types of chemistries:

1. Poly-A-tail based capture of native transcripts: Suitable for fresh-frozen samples only. These assays are NOT species-specific.
   2.) Probe-based “templated ligation”, capture, and amplification: Compatible with fresh-frozen, fixed-frozen, and FFPE tissue. Whole-transcriptome assays are available for human and mouse. Custom probe-sets can be generated for other species, including plants. This assay enables simultaneous analysis of both RNA and protein expression.

The Element Bio AVITI sequencer has seen a range of improvements. Upgrades have extended the read length (up to PE300 and 300 million read pairs at high quality) and enhanced the speed of the sequencer. Due to high demand, we have added a second AVITI sequencer to our lab. These sequencers are fully compatible with Illumina sequencing libraries.

Element Bio will start shipping UltraQ reagents this quarter that will enable sequencing at Q50 quality on the AVITI – this translates to about 100 times improved accuracy compared to standard Q30 data.

We would like to gather feedback with regard to current and coming technical options regarding cyto-profiling and spatial multi-omics.  
 

a) In situ hybridization based multi-omics systems currently offer the highest spatial resolution and sensitivity (down to the single-molecule level and sub-cellular resolution), while being If your research would benefit from the capabilities of instruments like the 10XGenomics Xenium please contact us.

b) Element Biosciences announced that the AVITI sequencers (after a significant hardware upgrade to AVITI24 status) will allow High Content Cellular Profiling and Cell Morphology Analysis also called cyto-profiling.  This enables multi-omics studies of up to 12 cell cultures per flowcell. Please see this presentation for the first details:   https://vimeo.com/912753106

Please contact the Genome Center director Blake Meyers (bcmeyers@ucdavis.edu) and the DNA Tech Core manager (lfroenicke@ucdavis.edu)  if you have interest in in situ hybridization based spatial multi-omics or cyto-profiling.