Abstract

Cellular
transcriptional profiles can readout a cells state, identity and response. Next-generation
sequencing methods can quantify transcript abundance at the single cell level
but lose valuable spatial information such as cellular position, interactions,
morphology and transcript subcellular location. Single molecule Fluorescence in
Situ Hybridization (FISH) imaging methods maintain such information but with allow
analysis of limited numbers of transcripts. Multiplexed Error-Robust FISH (MER-FISH)
adopts a spectral barcoding approach, facilitating the measurement of hundreds
to thousands of RNA species in single cells. We have scaled MER-FISH into a
high-throughput format allowing high dimensional readouts from cellular assays.
We have generated robust data across multiple cell lines which showed good
correlation with RNAseq measurements. Further, we have employed high-plex
MER-FISH to assay CRISPR and small molecules perturbations to validate target pathways
and understand compound specificity in cancer cell lines.