Services

DNA Sequencing

• Whole genome sequence
• Amplicon sequencing
• Whole plasmid sequencing
• Targeted resequencing
• Methylation analysis

Sample Preparation

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

RNA Sequencing

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

• Whole transcriptome
• Full-length transcriptome (Iso-seq)
• miRNA/smallRNA
• single cell gene expression
• spatial transcriptomics

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.

Data Analysis

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

Contact the Bioinformatic Consulting Center for analysis services

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 NextSeq 2000 - The NextSeq 2000 is a mid-throughput short-read, benchtop DNA sequencer.
• Illumina MiSeq - The MiSeq is a compact, short-read, benchtop DNA sequencer.
• PacBio Revio - PacBio's Revio is a high-throughput, long-read DNA sequencer.
• Oxford Nanopore Technologies MinION - The ONT MinION is a small device that allows for direct sequencing of native DNA

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 QuantStudio 5 PCR System - Benchtop quantitative real-time PCR machine available in 96 well and 384 well 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 - 4 PM, M-F. Sequencing results for individual Sanger samples should be available by 6 PM the same day. However, data for samples provided in 96-well plates may not be ready by 6 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