These data further revealed brain structures with especially rich isoform specificity. For example, the choroid plexus and hippocampus showed specific or preferential isoform expression across many genes.

Our isoform-resolved single-cell spatial transcriptomics data revealed widespread spatial and cell-type-specific isoform usage across the brain, with many genes showing distinct isoform enrichment in different anatomical regions and/or cell types.

Our whole-transcriptome-scale imaging data revealed spatially organized gene programs, cell-type- and region-specific differential expression, and ligand-receptor-based cell-cell communication patterns across the brain.

Integrating RT&T-AMP with multiplexed error-robust fluorescence in situ hybridization, (MERFISH), we imaged ~23,000 genes and ~10,000 isoforms in single cells in brain tissues with high spatial resolution.

We developed an in situ RNA amplification method, RT&T-AMP, that uses reverse transcription followed by transcription to generate amplicons at original transcript sites with uniform transcript body coverage, enabling to imaging of short RNA sequences anywhere along transcripts.

Delighted to share this preprint from Prof. Rong Fan Lab @RongFan8 and Prof. Sidi Chen lab @sidichen on Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT. Congatulations, Alev, Xiaolong, Feifei, Paul, Sidi and Rong!

Check out our preprint on Perturb-multi (doi.org/10.1101/2024.11.18.6…), a multi-year collaborative effort that enabled multi-modal in vivo genotype-phenotype mapping by pooled genetic perturbations and high-dimensionality phenotype readout by imaging and sequencing.