Vizgen Launches Data Release Program, Shares Spatial Genomics Mouse Brain Map
By Allison Proffitt
May 20, 2021 | Vizgen has released its first freely-available dataset as part of its newly-launched Vizgen Data Release Program. The Vizgen MERFISH Mouse Brain Receptor Map is an open-source spatial genomics dataset containing the exact position of transcripts from 483 genes across three full coronal slices with three biological replicates for each slice.
The dataset was generated with Vizgen’s MERSCOPE platform, a commercially-available platform comprising reagents and consumables, fully automated analytical instrumentation, and data visualization software, all designed for running MERFISH experiments.
MERFISH technology—multiplexed error robust fluorescence in situ hybridization—is massively multiplexed single molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to thousands of RNA species across hundreds of thousands of individual cells. The technology was developed at Harvard University and licensed by Vizgen in 2019. Earlier this year, Vizgen announced the MERSCOPE platform at AGBT.
The new Data Release Program is part of Vizgen’s efforts to expose the research community to the power of spatial genomics.
“Spatial genomics is still an emerging field, and it is not intuitive for those who have never worked with this type of data before to understand what spatial genomics measurement enables, and what they can do with the data,” explained Jiang He, Vizgen Co-Founder and Director of Scientific Affairs. “Data releases like this will help educate the research community on the type of data generated and provide relevant insights on the kind of discoveries that are enabled through spatial genomics data.”
Each dataset released will be freely available to participants to use as they wish, and will represent a different “cell atlas,” expanding on the global initiative to generate systematic and comprehensive reference maps of cells and how they function together in both normal and diseased biological tissues.
“As a company, Vizgen’s mission is to deliver the best tools for spatial biology that enable discoveries to improve human life,” He said. “Our data release program will really help drive this mission, providing researchers early access to MERFISH data to enhance their research and better understand the unique advantages of MERFISH.”
The MERFISH Mouse Brain Receptor Map that Vizgen is making available provides detail about the spatial expression of hundreds of receptor genes, notoriously difficult data to capture due to many of these genes being expressed at very low levels within the tissue. In all, the whole dataset contains 554,802,908 transcripts and 734,696 cells. The data set also includes cell boundary polygons, and high resolution DAPI and Poly T mosaic images.
The dataset, “represents a panel of 483 total genes including canonical brain cell type markers, GPCRs, and receptor tyrosine kinases,” He explained. “GPCRs have already proven to be valuable for drug targeting. However, many of them are lowly expressed, which has made this research challenging. MERFISH technology offers high sensitivity, true single cell resolution and high cell throughput, making it possible to detect lowly expressed, but functionally important, GPCRs that have been difficult to characterize through traditional techniques like scRNA-seq. As MERFISH enables highly multiplexed measurement, with panel size up to 500 genes, this dataset also demonstrates how we could use a targeted approach to make new discoveries.”
He says this with be the first of many datasets released as part of the Data Release Program. While he couldn’t commit to a timeline or specifics for the next data release, He did give some hints. “We do hope to release a dataset that is more clinically relevant, ideally in human cancer tissue samples,” he said. “Tumor is highly heterogenous, with many different cell types intricately organized in 3D. Having the ability to identify and map cell types in complex tissue like tumor and characterize their gene expression profile will shed light on the onset, progression and even drug response for this devastating disease, and MERSCOPE’s high multiplexing power, single cell resolution and high sensitivity is uniquely suited for this purpose.”