Whole Transcriptome Atlas

A new way to look at biology

The WTA panel provides whole transcriptome coverage with probes specific to protein coding mRNA sequences. These sequences are based on the HUGO database and cross-referenced with the NCBI RefSeq database to give you confidence in each transcript. Along with a high specificity for their target molecules, DSP RNA probes are screened for a myriad of factors including melting temp, GC content, off target hits, and repetitive sequences. Each probe is assigned a unique DSP barcode for downstream molecular counting on the Illumina sequencer. The targeted nature of this panel avoids the many pitfalls of poly(A) pulldown techniques by delivering increased sensitivity even in heavily degraded tissues such as FFPE.

With GeoMx, researchers can explore pathways across the whole transcriptome in user defined regions of interest. Providing an unbiased view of 18,000 protein-coding genes, the WTA can unlock new pathways to e explored and enables RNA profiling in oncology, immunology, neuroscience, developmental biology and other diverse fields.

With 18,000 genes to target, its also important for the probes to be sensitive and also accurate enough to confidently count. GeoMx RNA assays contain in situ hybridization (ISH) probes conjugated to unique DNA indexing-oligonucleotides via a UV-photocleavable linker. After selecting regions of interest (ROIs), the DNA oligonucleotides are UV cleaved and then sequenced on an Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed then imported back into the GeoMx platform for integration with the slide images and ROI selections for spatially-resolved RNA expression.