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Genomics Facility

Overview

The Genomics Shared Resource serves as a hub for consultation and scientific interaction relating to nucleic acid-based methods. It provides expertise and support to ensure the best possible outcomes for genomic-related projects. The Facility supports several state-of-the-art platforms for a wide variety of nucleic acid-based studies, including massively parallel sequencing and routine capillary sequencing. The Facility also supports projects related to RNA sequencing, ChIP-Seq, smRNA-Seq, whole genome, exome and targeted resequencing, bulk TCR and BCR immune repertoire profiling, methylation (MeDIP), single cell sequencing, and gene expression studies using Quant-seq or the NanoString platform. In addition, we support SNP genotyping analysis using TaqMan assays, KIR allele genotyping, HLA typing and microsatellite assays. Consultation is provided to assist with experimental design and for the development of custom services.

Services

  • Illumina Next-Generation Sequencing (NextSeq 500 and MiSeq)
    • Gene Expression Analysis: Lexogen QuantSeq3’ mRNA-Seq library prep kit is used to generate Illumina-compatible libraries    
    • Transcriptome analysis applications: RNA-seq, RNA-IP-seq, small RNA-seq
    • Genome sequencing
    • ChIP-seq
    • DIP-seq
    • MeDIP and hMeDIP
    • Exome and Amplicon sequencing
  • BCR and TCR immune repertoire profiling
  • Targeted sequencing
  • Single cell gene expression analysis, single cell immune profiling, scATAC-Seq
  • NanoString nCounter platform
    • Multiplexed digital quantification of nucleic acids without sample amplification. 
    • Applications for gene expression, miRNA, SNPs and CNV.
  • Single-cell analysis system
    • Takara Bio iCell 8 single cell Nanodispenser: MultiSample NanoDispenser (MSND) deposits nanoliter volumes of cells and reagents into the ICELL8 Chip in a temperature and humidity-controlled environment. MSND is capable of dispensing eight unique samples evenly across the chip. Hundreds of live single cells are captured for downstream NGS applications: 3’ single cell and full-length single cell gene expression applications.
    • 10x Genomics Chromium Controller: The chromium system uses GemCode technology to enable thousands of microreactions in parallel. A two-step partitioning process allows thousands of single cells and their transcripts to be uniquely barcoded and then pooled for downstream processing and library preparation for single cell gene expression analysis, immune repertoire profiling and epigenetic studies. Feature barcoding technology uses specific oligonucleotide sequences to identify cell surface proteins and CRISPR alterations.
  • Digital PCR: The QX200 Droplet Digital PCR system enables absolute quantification of targets by partitioning a qPCR reaction into millions of picoliter-sized droplets such that each droplet contains either 0 or one molecules of interest. Every droplet is measured for fluorescence to generate a negative or positive signal, providing a true digital result.
  • Capillary DNA sequencing
  • 16-panel microsatellite analysis
  • HLA typing
  • KIR allele genotyping
  • C. bovis Detection
  • qPCR services using Taqman assays
  • SNP genotyping analysis
  • Additional Services:
    • RNA and DNA preparation and quality control for all services
    • NGS library preparation
    • Experimental consultation and project troubleshooting

Equipment & Features

  • Illumina NextSeq 500
  • Illumina MiSeq
  • 10x Genomics Chromium Controller
  • Takara Bio iCell8 Single Cell Analysis System
  • NanoString nCounter Analysis System
  • ABI 3130xl
  • Covaris High Performance Ultrasonicator
  • GE Healthcare Bioscience ImageQuant LAS4010
  • Agilent TapeStation
  • Agilent 2100 Bioanalyzer
  • Integra Assist Plus liquid handler

Pricing

For pricing information, visit iLab or contact the managing director.

This facility is supported in part by a Cancer Center Support Grant (CCSG) awarded by the National Cancer Institute (NCI) to The Wistar Institute Cancer Center.

Click here for information on how to acknowledge our Shared Resources in your publications and grants.

Contact Us

The Wistar Institute
Genomics Facility, Room 284
3601 Spruce Street
Philadelphia, PA 19104
215-898-3902
genomics@wistar.org

Facility Hours:
9:00 a.m.-5:30 p.m., Monday-Friday

Louise C. Showe, Ph.D.
Scientific Director

Sonali Majumdar, M.S.
Managing Director

Shashi Bala, Ph.D.
Wistar Scientist
Illumina/Next Gen Sequencing