University of Pennsylvania Gene Therapy Program - Nucleic Acid Technologies Core

The Core is equipped with instrumentation for complete NGS pipelines consisting of four short read Illumina sequencers (1 million to 1.3 billion reads), one NanoPore MinION sequencer, and instruments for NGS sample preparation (Covaris ultrasonicater, BluePippin) and sample/library quality control (Qiaxcel, Bioanalyzer, Qubit, Tapestation 4200). Introduced in 2021, the Core began performing single cell analysis services using the 10X Genomics Chromium platform for both scDNA and scRNA analysis from cell suspensions.

Serving both discovery and translational research groups at GTP, our team currently processes hundreds of NGS samples every month. In addition to wet lab services, the Core routinely performs data analysis and reporting of on- and off-target effects of genome editing, complete plasmid and vector genome sequencing (research, production, and IND-enabling grade). We also work closely with study directors, bioinformaticians and biostatisticians at GTP to support timely in-depth NGS data analysis for complex projects.

Services Performed

Design and execution of novel custom NGS workflows
Consultation in NGS experimental design, data interpretation, and troubleshooting
NGS library prep, QC, and sequencing for:
- Plasmid sequencing
- Vector genome sequencing
- Amplicon sequencing
- AMP-seq (Anchored multiplex PCR followed by NGS)
- Whole exome and whole-genome sequencing
- Bulk RNA-seq
- Long read sequencing using Oxford Nanopore workflows
- Single cell analysis workflows: 10X 3’ Gene Gene Expression, 10X ATAC-seq, 10X Multiome
Data analysis and reporting of indel analysis, on and off-target effects of genome editing, plasmid, and vector genome sequencing
10X Cell Ranger analyses for single cell workflows
Basic analysis (base calling and read alignment) for long read sequencing (Oxford Nanopore Technologies)
Training on nucleic acid quality control (Bioanalyzer, Qubit, Qiaxcel, Tapestation-4200)