Data from: Protocol optimization improves the performance of multiplexed RNA imaging

Spatial transcriptomics has emerged as a powerful tool to define the
cellular structure of diverse tissues. One such method is multiplexed
error robust fluorescence in situ hybridization (MERFISH). MERFISH
identifies RNAs with error tolerant optical barcodes generated through
sequential rounds of single-molecule fluorescence in situ hybridization
(smFISH). MERFISH performance depends on a variety of protocol choices,
yet their effect on performance has yet to be systematically examined.
Here we explore a variety of properties to identify optimal choices for
probe design, hybridization, buffer storage, and buffer composition. In
each case, we introduce protocol modifications that can improve
performance, and we show that, collectively, these modified protocols can
improve MERFISH quality in both cell culture and tissue samples. As RNA
FISH-based methods are used in many different contexts, we anticipate that
the optimization experiments we present here may provide empirical design
guidance for a broad range of methods.  The data provided in
these repository are those used in the optimization and validation of
these protocols.