Technologies

To acknowledge use of this shared resource, please include the following in your publications: This research was partially supported by UNM Comprehensive Cancer Center Support Grant NCI P30CA118100 and made use of the Analytical and Translational Genomics Shared Resource, which receives additional support from the State of New Mexico.

Next-Gen Sequencing

Applications of Next-Gen Sequencing

Next-generation (massively parallel) sequencing is useful for a variety of experimental approaches. It is not a replacement for normal (Sanger) sequencing of plasmids or PCR products. Instead, next-gen sequencing relies on capturing millions or billions of individual DNA molecules (e.g. genomic DNA fragments, cDNAs), which are then amplified separately and sequenced in parallel, generating millions or billions of sequencing "reads", each of which originated from a different template molecule. It is similar to individually cloning and sequencing millions or billions of independent DNA fragments, but it all happens at once and in just a few days.

The following types of scientific applications are easily adaptable to next-gen sequencing approaches:

  • Targeted gene panel sequencing of cancer- or disease-relevant genes • Gene expression studies using RNA-seq
  • Chromatin Immunoprecipitation - sequencing (ChIP-seq) for transcription factor or epigenetic studies
  • DNA methylation studies (e.g. RRBS)
  • Transcriptome sequencing (e.g. identification of alternatively-spiced RNAs)
  • Analysis of non-coding RNAs (ncRNAs, lincRNAs, miRs)

Technologies and Instruments

The ATG facility currently has or has access to several types of next-gen sequencing instruments:

• Ion S5/XL: A solid state NGS insturment generating up to 100 million reads per chip

These instruments provide cost-efficient and rapid next-generation sequencing for applications such as targeted sequencing, RNA-seq, ChIP-seq, MeDIP-seq and even low-pass whole-genome sequencing for copy number variant analysis.

Instruments

Shared instruments available Mon-Fri 8:30 am - 5 pm

(other times may be available by special arrangement)

The KUGR Facility has several unique instruments that UNM researchers can arrange to use. Qualified laboratories pay an annual user fee and receive training and support from KUGR Staff. The instruments are available for use in the facility during normal working hours.

Agilent Bioanalyzer: An important instrument for molecular biologists, replaces gel electrophoresis for many types of applications. It is especially useful for analyzing the quality and/or quantity of RNA or DNA samples using very small amounts of material, instead of running large amounts of precious sample on a gel.

Nanodrop Spectrophotometer: A droplet spectrophotometer that measures absorbance in a small droplet of sample. This avoids the need to dilute samples into large cuvettes.

Qiagen Qiacube Robot: A dedicated sample preparation robot for performing RNA and DNA isolation and purification steps with Qiagen kits.

Please contact the KUGR Facility staff for more information about assays and pricing.