Illumina Hiseq 2500

The UAGC offers a variety of Illumina HiSeq2500 supported applications including Shotgun/de novo sequencing, RNAseq, Exome sequencing, Small RNA profiling as well as other custom NGS pipelines.

General Information


Sample Input

DNA or RNA from a variety of sample types can be run on Illumina HiSeq 2000/2500 including cells, tissue, and blood. We also offer DNA or RNA extraction for library prep.

Applications include:

  • Whole Genome Sequencing (Shotgun/de novo)
  • Other supported and custom protocols (please inquire)
  • Metagenome Analysis
  • CHiPseq
  • miRNA profiling
  • Mate Pair Sequencing (3kb, 5kb, 10kb)
  • Exome Sequencing
  • RNASeq (transcriptome sequencing)

Expected Results

  • Read length - 2x100bp PE (paired end), 1x50bp SR (single read), 2x50bp PE, 1x100bp SR
  • Average data output - 30GB per lane (2x100PE)

Data Delivery: Data may be accessed using the UA HPC or downloaded to your machine via Cyberduck. See the following user guides for detailed instructions: Cyberduck User Guide OR HPC-iRODS User Guide

  • Untrimmed reads
  • Fastqc_out folder containing zipped quality reports
  • Reads trimmed by Trimmomatic
  • Organized into paired reads and reads whose pair was not retained due to quality trimming
  • In addition to trimming Illumina adapter sequence, trimmomatic parameters used are: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15

Details


Sample Preparation Details

DNA sample requirements (if not submitting tissue, cells, etc. for extraction):

  • 100ng-3µg total DNA required (shotgun/de novo and Exome sequencing)
  • DNA should contain no particulate matter
  • DNA should not be the result of whole genome amplification (or other process that can compromise accurate representation)
  • DNA must be double-stranded
  • DNA should have an OD 260/280 ratio ≥ 1.8
  • DNA should not be degraded
  • DNA sample should be suspended in LowTE or water
  • 15µg total DNA for 10kb mate pair libraries
  • 10µg total DNA for 3kb and 5kb mate pair libraries

RNA sample requirements:

  • 100ng-3µg total DNA required
  • RNA should be resuspended in RNAase free water or RNA preservative
  • RNA should not be degraded

Workflow


Complete the Request a Quote form and we will contact you to discuss your project workflow.

Quality Control of Samples: Every sample received for sequencing will go through a set of quality control checks before it can be processed. Customers may be asked for more DNA/RNA if their sample fails either of the following checkpoints:

  • Pico/RiboGreen Assay to verify the quantity of starting material
  • Bioanalyzer DNA/RNAchip to check the material quality

Cluster Generation for Prebuilt Libraries: Cluster generation run submissions must be greater than or equal to 10nM post library construction concentration

Sequencing Chemistry: The UAGC uses Illumina TruSeq SBS chemistry

Library Preparation/Construction: UAGC uses a variety of DNA/RNA library construction kits Maximum 2048 samples multiplexed per lane (UAGC provides MD tagging)

*Note: Per Illumina recommendations we cannot run libraries that are more than 6 months old. Therefore, your library material will be disposed of 6 months after they are built in accordance with our SOPS.

Data Analysis: Supplementary data analysis will incur additional labor rates. Please contact Genome Analytic Services to discuss further data analysis needs.

Price

Library Prep-

Academic (UA): $390.00 | Academic (non-UA): $468.00 | Industry: $585.00 | Unit: Library

 

Sequencing-

Academic (UA): $2400.00 | Academic (non-UA): $2880.00 | Industry: $3624.00 | Unit: Lane (2x100PE)

Turnaround Time

Average turnaround time will vary dependent upon application and sample input.

Average data turnaround time for most NGS projects is approx. 4-6 weeks.

The UAGC operates on a first come, first serve entry into sample queue.

Related Services

High Recovery DNA Extraction

RNA Extraction and analysis (Agilent Bioanalyzer 2100)

Sanger DNA sequencing for validation of NGS 

Additional Information

If there is a specific application you are interested in on the HiSeq2500 but do not see listed here, please contact us to see if we can accomodate your needs!

University Customers: We are located in Keating Building Room 124. Samples may be left in the freezer at the north entrance to our lab. Samples should be clearly labeled "Illumina" along with your contact information and billing account.

External Customers: Samples should be shipped pre-frozen and preferably on dry ice (although regular ice packs work well enough for overnight shipping). Sample tubes should be sealed with parafilm.

Shipping Address:
University of Arizona Genetics Core
ATTN: Illumina NGS
1657 E. Helen St.
Keating Building, Rm 106
Tucson, AZ 85721