Question: What library types can be pooled prior to hybridization in the Targeted Gene Expression assay?
Answer: The Targeted Gene Expression assay generates targeted libraries from Whole Transcriptome Analysis (WTA) input libraries. Supported input library types include:
- 3’ Single Cell Gene Expression libraries (v3, v3.1 and dual index v3.1)
- 5’ Single Cell Gene Expression libraries (v1, v1.1 and v2)
- Coming soon: we are currently developing an optimized protocol for using Spatial Gene Expression libraries as input libraries
For the Targeted Gene Expression assay, up to eight WTA input libraries can be pooled prior to hybridization.
For optimal assay performance, we recommend pooling input libraries prepared from similar cell types, similar cell loads, and using the same chemistry (3' versus 5') and indexing strategy (single index versus dual index).
- While pooling libraries from different cell types and pooling 3' and 5' Gene Expression libraries is compatible with the Targeted Gene Expression assay, it can lead to sequencing read imbalance.
- Pooling single index and dual index libraries can introduce additional complexity due to varying read configurations required for sequencing.
Do not pool libraries with the same sample index, as pooled libraries will be sequenced together. For adequate sample demultiplexing post-sequencing, each library must contain a unique sample index.
Products: Targeted Gene Expression