Computational and molecular biology team

Established in-house molecular biology, genomics, and bioinformatics efforts.• Barcoded mRNA design and productionDeveloped barcoded mRNA manufacturing methods to produce hundreds of milligram-scale barcoded mRNAs/nucleic acid delivery models to track LNP/mRNA delivery/bioaccumulation in small-animal models.• Next generation sequencing coreFormed genomics team, established genomics lab, and developed protocols to extract and sequence hundreds of tissue samples in-house from small animal models to quantify LNP/mRNA delivery/bioaccumulation using high-throughput sequencing (NextSeq 1000 and Oxford Nanopore).• Bioinformatics and data analysisWrote all pipelines; analyzed, and visualized all MPRA data to determine LNP bioaccumulation and mRNA stability in various tissues and cell-types.

Mitchell Laboratory

Genomics and Computational Biology Team (GACT)Interfacing with therapeutic groups to develop, plan, execute, and analyze:• Single-cell/bulk transcriptomics and gene regulation to characterize therapeutic products and gene editing targets.• Spatial transcriptomics experiments to characterize therapeutic products in vivo/in vitro• Long-read assays characterize therapeutics products• Massively parallel reporter assays to improve targeting and expression of therapeutics.• Off-target nomination assay development

Genomics Innovation Hub

Soloway Laboratory • Changes in cellular heterogeneity in Down syndrome using single-cell ATAC-seq:Using modified single-cell combinatorial indexing assay for transposase accessible chromatin using sequencing (sci-ATAC-seq), characterized changes in cell-type representation and gene regulation in the cortex of Down syndrome model mice.• DNA methylation at transposase accessible chromatin using methyl-ATAC-seq:Developed methyl-ATAC-seq, a novel variant of ATAC-seq, to simultaneously measure DNA methylation and chromatin accessibility at transposase accessible chromatin. Assayed DNA methyltransferase-deficient cells to characterize methylation-sensitive transcription factors and loci.• RNA-binding protein interactions at the Rasgrf1 imprinting control region:Isolated, identified via LC/MS, knocked out using CRISPR/Cas9, and characterized proteins bound to a lncRNA demonstrated to direct imprinting at Rasgrf1 (pit-RNA).• LNP delivery tracking:Designed and produced mRNA barcoding system to track functional mRNA lipid nanoparticle delivery to organs in mice.

Genomics Core Laboratory (GCL)• RNA-seq and targeted-exome library preparation and analysis of Illumina, SOLiD, and Ion Torrent machines. Illumina and Affymetrix microarray library prep and analysis. Designed and piloted digital PCR-based assays for detection of cell-free tumor DNA.

Pearse Laboratory • MLK3 phosphorylation in multiple myeloma:Studying the role of MLK3 (MAP3K11) phosphorylation in multiple myeloma from isolated CD138+ primary cells for drug targets via targeted shRNA knockdowns.• Multiple myeloma metabolome:Studying metabolic changes in CD138+ cells isolated from multiple myeloma patients and cultured myeloma lines using LC/MS.

Ballas Laboratory • Glial dysfunction in Rett syndrome:Using Rett syndrome model mice deficient in methyl-CpG binding protein 2 (MeCP2) to study the interaction between MeCP2-/- derived astrocytes on neuronal morphology using immunofluorescence in an in vitro co-culture system.• Roles of REST and CoREST in maintaining ES pluripotency and differentiation:Knocked down RE1-silencing transcription factor (REST) and CoREST in in vitro differentiated embryonic stem cells to investigate their role in neuronal lineage commitment using immunofluorescence and RT-qPCR.

Citovsky Laboratory• Tobacco mosaic virus movement protein transportTransfected, via biolistic bombardment, and transduced via Agrobacterium Infiltration, Tobacco plants with fluorescently tagged ankyrin repeat-containing protein and Tobacco mosaic virus movement protein to characterize their role in mediating cellular transport under the supervision of Dr. Shoko Ueki via immunofluorescence, western blot, and RT-qPCR.