Genomics

info
For More Information
Contact Ning-Lin Yin: (435) 797-8218; ninglin.yin@usu.edu or Aaron Thomas: (435) 757-5534; aaron.thomas@usu.edu

The Genomics laboratory is a core facility of the Center for Integrated BioSystems at Utah State University. The genomics core is a shared resource that provides genomics services to investigators on campus and external users. The facility offers state-of-the-art resources and services, including Next Generation Sequencing using our Illumina MiSeq, Ion Torrent Proton, and Ion Torrent PGM systems. In addition, a range of traditional DNA sequencing and fragment analysis options are available using our ABI PRISM™ 3730 DNA Analyzer. The Genomics Core also offers analysis services using Affymetrix Microarray Technology for gene expression profiling. Other services include RNA and DNA analysis (Agilent TapeStation), quantification (NanoDrop and Qubit), and size selection (Sage Science Blue Pippin 50-50,000 bp). We strive to provide all of our customers with fast, accurate results. For inquiries please contact Ning Lin Yin.


Next Generation Sequencing

The Center for Integrated Biosytems offers next generation sequencing services on the Illumina NextSeq, and Illumina MiSeq. Applications include whole genome sequencing, RNA-Seq, methylation analysis, amplicon sequencing, genotyping by sequencing (GBS), microRNA sequencing, 16S ribosomal sequencing, ChIP-Seq, targeted sequencing, and more. We also offer size selection on the Blue Pippin automated size selection platform.

Services

Blue Pippin Size Selection

The Blue Pippin is capable of selecting 100-50,000 bp fragments. However, we do not routinely have the supplies for size selection above 600 bp. Please contact us if you need selection of fragments above 600 bp. Samples are $15 each. Subsequent analysis on the TapeStation is an additional $5 per sample.

Library Preparation

We offer standard library preparation for RNA-Seq, microRNA, and whole genome sequencing samples. For other sequencing types, we can assist you with designing your protocol and can work with you as needed to sequence your samples.

  • DNA library (e.g. whole genome) - $90
  • RNA-Seq - $110
  • microRNA - $130

Sequencing

While we strive to achieve the best results possible, the listed number of reads is the specification published by Illumina and individual runs may vary from these numbers.

The listed read length can be changed if necessary. Please contact us if you need something different.

Illumina MiSeq

MiSeq Reagent Internal USU Price External Price Expected Read Number Typical Read Length
Kit v3 (150 cycle) $1,250 $1,750 25M 2X75
Kit v3 (600 cycle) $1,970 $2,760 25M 2X300
Kit v2 (50 cycle) $1,145 $1,600 15M 1x50
Kit v2 (300 cycle) $1,410 $1,975 15M 2X150
Kit v2 (500 cycle) $1,560 $2,185 15M 2X250
Micro Kit v2 (300 cycle) $675 $990 4M 2X150
Nano Kit v2 (300 cycle) $510 $750 1M 2X150
Nano Kit v2 (500 cycle) $575 $840 1M 2X250

Illumina NextSeq

NextSeq Internal USU Price External Price Expected read number Typical read length
Mid Output Kit v2 (150 cycles) $1,450 $2,030 130M 2X75
Mid Output Kit v2 (300 cycles) $2,215 $3,100 130M 2X150
High Output Kit v2 (75 cycles) $1,915 $2,680 400M 1X75
High Output Kit v2 (150 cycles) $3,485 $4,880 400M 2X75
High Output Kit v2 (300 cycles) $5,460 $7,650 400M 2X150

 


Affymetrix GeneChip® System

Affymetrix GeneChip® microarray services, known to be highly reproducible, accurate, and reliable, are used for gene expression analysis. Affymetrix analysis is used for a broad and expanding list of applications, allowing researchers to study expression for any number of genes in any model organism. For additional instructions, see Affymetrix Sample Preparation and Affymetrix Package and Sample Delivery.

Sample Submission Forms

Sample Preparation

Services

  1. Standard Service
    CIB full-service includes quality control, labeling, and fragmenting. QC re-evaluation occurs before intermediate steps (hybridization, washing, staining, and scanning) are performed. QC reports and data are returned to customer.
  2. Minimal Service
    CIB minimal service uses customer-supplied labeled and fragmented samples. CIB will perform QC re-evaluation before intermediate steps (hybridization, washing, staining, and scanning). QC reports and data are returned to customer.
GeneChip System

Additional Bioanalysis services available upon request.

 


DNA Sequencing

The genomics group offers high quality and fast turnaround on DNA sequencing services using an ABI PRISM™ 3730 DNA Analyzer. The 3730 utilizes BigDye terminator chemistry. Standard primers (M13 / T7 / T3 / and SP6) are available. Turnaround times vary based on services. Sequencing data will be emailed to customers, or available on the facility server.

Services

RUSH: Samples received before 9 a.m. will be returned by 5 p.m. (extra charges apply)

  • Reading DNA/Primer conc. & adjusting dilutions ($8.50 to $10.50)
  • Performing sequencing PCR reactions
  • Running the sequencing reactions ($6.00)
  • Purification of sequencing PCR reactions ($3.75) x 96 well request
  • Loading only (3730) and sending data ($1.00)
  • Data turnaround in 1-2 business days

High Volume 96-well
Price List of Reagent and Consumables from 454

dna analyzer

 


Fragment Analysis

The genomics group offers Fragment Analysis services with our ABI PRISM™ 3730 DNA Analyzer. The 3730 employs an array of 48 capillaries to electrophoretically separate fluorescently labeled DNA fragments. A number of different services are available for the automated analysis.

Sample Submission Forms

Services

  • Microsatellite variation analysis
  • AFLP analysis
  • RLP analysis
  • STR analysis
  • SNP analysis
dna analyzer newer version

 


RT-PCR

The genomics group offers quantitative PCR as a two tier service using the DNA Engine Opticon 2.

Sample Submission Forms

Services

  • Customer driven service. CIB will program customer plates and protocol.
  • CIB genomics group driven service. CIB will set-up the experiment from start to finish using your primers and template. Software and technical support for your data analysis is available.
DNA Engine Opticon 2

 


RNA/DNA Quality Control/Quantification

The genomics group provides fast, reliable, and convenient services for RNA and DNA quality control and concentration quantification. Eleven samples for RNA and DNA QC can be turned around in just two hours.

Standard Running Cost: ~ $80 per chip / (1-11 samples)

Bio-Rad Experion

Sample Submission Forms

Services

  • Agilent 2200 TapeStation
    The Agilent 2200 TapeStation is an automated electrophoresis system for the sample quality control of DNA and RNA samples. The reagents we keep on hand are: Hight Sensitivity D1000 DNA ScreenTape, with a as low as 5 pg/µl. If you need other TapeStation analysis (different sizing, high sensitivity RNA, et.) contact sensitivity aaron.thomas@usu.edu to discuss availability.
    Cost: $10 per group of 2 samples.
  • Agilent 5200 Fragment Analyzer
    The Agilent 5200 Fragment Analyzer is a capillary electrophoresis instrument for DNA analysis. The standard analysis reagents we keep on hand have a sensitivity down to 0.5 ng/µl. and sizing from 25-1500 bp.
    Cost: $20 per group of 12 samples.
    The instrument is capable of much more with other reagents. If you need other analysis, contact aaron.thomas@usu.edu to discuss your needs.
  • Thermo Scientific NanoDrop 8000
    NanoDrop™ 8000 (and NanoDrop 1000) are available for use by campus affiliates for a small fee. Equipment provides reliable data for analysis. Eight 1.5 ul samples can be measured at one time using spectrophotometer to measure full-spectrum UV-Vis absorbance. For training, contact genomics group.

Interpretation of Agilent 2100 Bioanalyzer Data (PowerPoint Presentation)