Services

DNA Sequencing

• Targeted resequencing
• Whole-genome resequencing
• Chromatin immunoprecipitation (ChIP-Seq) analysis
• Methylation analysis

Sample Preparation

Sample requirements vary somewhat depending on the application. Please contact the facility for details.

Data Analysis

Raw data is provided to the customer for analysis, as the facility does not provide data analysis services.

• NextGene and LifeScope software packages are available free of charge for “DIY” analysis.

Instrumentation

The Facility currently supports the use of the following three next–generation sequencing platforms, and will provide guidance in choosing the platform that best suits your project.

• Illumina HiSeq 2500 -- This next-generation sequencing instrument produces medium-length reads and can be used for a variety of applications.
• Illumina MiSeq -- This instrument is essentially a small version of the HiSeq 2500.

RNA Sequencing

RNA sequencing applications supported by the Genomics Core Facility include, but are not limited to:

• whole transcriptome,
• miRNA/small RNA,
• degradome,
• RIP-Seq, and
• de novo transcriptome sequencing.

The customer must simply provide the facility with high-quality RNA, and the facility will make libraries from the samples and sequence them on the appropriate platform depending on the application.

Sample Preparation

General recommendations for RNA isolation and the determination of concentration, purity, and quality can be found in our RNA sequencing sample preparation recommendations. Sample requirements vary somewhat depending on the application. Please contact the facility for details.

Services

The Genomics Core Facility provides real-time DNA and RNA quantification services using real-time qPCR.

Data Analysis

Please note: the facility does not provide data analysis services.

Instrumentation

• Applied Biosystems 7300 Sequence Detection System -- Platform for detection and quantification of nucleic acid sequences
• Applied Biosystems 7900HT Fast Real-Time PCR System -- The acknowledged gold standard in real-time PCR
• Applied Biosystems OpenArray Real-Time PCR Instrument and AccuFill System -- Best combination of convenience, flexibility, throughput, and cost-effectiveness for mid-density genotyping, and gene expression and digital PCR studies

The Applied Biosystems Open-Array Real-Time PCR Instrument and AccuFill System offers the best combination of convenience, flexibility, throughput, and cost-effectiveness for mid-density genotyping, as well as gene expression and digital PCR studies.

Uses

• SNP determination
• Gene expression quantification
• Digital qPCR
• Copy number variation

Specifications

• Capable of processing thousands of samples per day, enabling mid-density, high-throughput results
• 3,072 determinations (33 nl volume) can be done per well
• Up to 8 plates can be run simultaneously
• Up to 144 samples per plate can be analyzed at a time

Details

• Digital PCR allows for highly accurate quantification of copy number and viral load
• Please inquire about plate formats

Services

• Regular sequencing: standard plasmid and PCR products as well as BACs and cosmids
• High-throughput sequencing: 96-well plate submissions

Specifications

Please inquire regarding specifications for submitting plates before submitting them.

Requests

All sequencing requests must be made using iLab. Samples should be dropped off from 8 AM - 1 PM, M-F. Sequencing results for individual Sanger samples should be available by 8 PM the same day. However, data for samples provided in 96-well plates may not be ready by 8 PM the same day.

Data Analysis

Please note: the facility does not provide data analysis services.

Instrumentation

Applied Biosystems 3730XL

VNTRs

VNTR alleles can be determined by fragment analysis on the 3730 XL DNA Sequencer. A 5-color system uses four fluorescent-labeled primers to multiplex PCR products in the same well. At minimum, four genotypes can be determined per sample in less than an hour for about $110 (96 samples in a 96-well plate).

Multiplexing different products with the same color can double or even quadruple the number of genotypes per sample (due to resolution of different-sized products with one base resolution). Allele or peak size is determined by using software such as Genemapper. Peak Scanner is another useful software program, and is available for free download from Applied Biosystems.

SNP Determination

SNPs can be determined by several techniques, including standard allelic discrimination (Taqman assays), open-array technology, and high-resolution melt curve analysis. Open-array technology can be used to determine 3072 SNPs for about 15-20 cents per SNP. High-resolution melt curve uses a dsDNA intercalator to determine homozygotes and heterozygotes by detecting small differences in PCR melting curves.

Instrumentation

Applied Biosystems 3730XL

Oligonucleotides ordered from Integrated DNA Technologies through this Portal are shipped to W102 Millennium Science Complex on the Penn State campus.

Click here to visit IDT

We have negotiated a discount on several products with GenScript if these are shipped to the below location (right beside IDT deliveries).

If you do not have a GenScript account yet, please set it up at this link.

• Pricing

For all new and existing end users, please use the following shipping address and information:

Craig Praul
cap142@psu.edu
W-102 Millennium Science Complex
Penn State University
University Park, PA 16802

Please directly email your requests to the GenScript team Eleanor.Li@genscript.com and Ningning.Shao@genscript.com (preferred method). You can also request a quote on the GenScript website.