Question: Can I pool libraries generated from short cDNA and long cDNA for use in the Spatial Targeted Gene Expression assay?
Answer: When using Visium Spatial Gene Expression libraries as input into the Targeted Gene Expression assay, it is important to follow the appropriate hybridization and wash protocol based on the average fragment length of the cDNA that was used to generate the parent Visium Spatial Gene Expression library. See: Why do I need to calculate cDNA length for the Targeted Gene Expression assay?
Up to eight Visium Spatial Gene Expression libraries can be pooled together prior to hybridization in the Targeted Gene Expression assay. If pooling Visium Spatial Gene Expression libraries generated from short cDNA with libraries generated from long cDNA, the “short cDNA workflow” should be followed for the hybridization and wash steps in the Targeted Gene Expression assay:
Given the possibility of batch effects between the “short cDNA workflow” and the standard workflow, we recommend following the same protocol for all samples to be compared within a given project. If analysis requires comparing Spatial Targeted Gene Expression libraries prepared from short cDNA with libraries generated from long cDNA, the “short cDNA workflow” should be followed for all samples.
Note: The Targeted Gene Expression assay has been discontinued. For alternative options, please see: What options are there for performing a targeted enrichment for my gene expression libraries?
Product: Targeted Gene Expression, Visium for fresh-frozen