Penn Functional Genomics Core

Overview

The Functional Genomics Core provides state-of-the-art experiment planning, sample preparation, quality assessment, library construction, DNA sequencing, and data analysis services to DRC members. We are currently operating five state-of-the-art Illumina Sequencers. We have experience with ChIP-seq, nucleosome mapping, miRNA, and genome resequencing in mouse, human, zebrafish, and other species. We offer RNAseq, microRNAseq, GroSeq, CLIP-seq, nucleosome mapping, ATAC-Seq, ChIPseq, Exome sequencing, whole genome and targeted methylome analysis, hydroxymethyl DIP, and single cell RNAseq. A second goal of the FGC is to quickly adapt and occasionally develop new protocols for sequencing-based functional genomics analysis relevant to DRC members.

Services

Next Generation Sequencing Core Services

For Next Generation Sequencing Core Services, please contact the Technical Director of the Core, Dr. Jonathan Schug Email

Services offered by the NGSC:

  • Experiment Design: Advice on techniques, sequencing depth, and analysis.
  • Quality Assessments: Agilent bioAnalyzer and TapeStation, Life quBit, KAPA Library Quant kit.
  • Library Preparation: Various protocols for Illumina sequencing.
  • Single-Cell Genomics: We have two single-cell capture technologies to choose from 10x Genomics and Fluidigm C1. The 10x Genomics Single-Cell Controller provide very high cell count data using a range of input cell counts. Using the C1 to capture single cells for RNA-Seq, WGA DNA-Seq, or Tag-man PCR. The C1 generally provides a richer transcriptome and can generate full length transcript data.Using the C1 to capture single cells for RNA-Seq, WGA DNA-Seq, or Tag-man PCR.
  • Data Analysis: Basic data analysis for sequencing data.
Computational and Bioinformatics Support Services

For complex Computational and Bioinformatics Support Services, only available to DRC members, please contact Dr. KJ Won Email

Services include but are not limited to complex transcriptome analysis of mRNA and miRNA gene expression, analysis of miRNA to mRNA targeting relationships, cistrome and methylome analysis and their integration, analysis of allele-specific gene expression and transcription factor binding, and analysis of nascent transcripts obtained by GroSeq.

Core People

Core Director
Klaus Kaestner PhD Penn Functional Genomics Core Email