Methods and Workflows

Long-read sequencing (SMART core)

• Base modification calling. Oxford Nanopore reads are basecalled with Dorado using modified-base models, producing BAM files that record 5-mC, 5-hmC, and 6-mA per read. We use adaptive sampling to enrich CpG islands and other targets from whole-genome libraries in real time.

• Direct RNA sequencing. ONT direct RNA-seq yields isoforms, splice junctions, long non-coding RNAs, natural antisense transcripts, alternative polyadenylation sites, poly(A) tail lengths, and RNA base modifications from a single dataset.

• snRNA-seq without specialized instruments. We use combinatorial barcoding (Split-seq) to build single-nuclei libraries that sequence with both short reads and long reads, targeting 2,000 to 3,000 nuclei per sample.

Proteomics (SAM core)

The foundational proteomics dataset is generated with the Yale Proteomics Core and the Yale/NIDA Neuroproteomics Center, with analysis tools for collection through interpretation, including methods for the partial diallel design.