RII Core Facilities
University of Arizona
PO BOX 210240
Tucson, AZ 85721

Email: CoreBusiness@email.arizona.edu

Taqman SNP Genotyping is a robust and economical method to type a small number of Single Nucleotide Polymorphisms, SNPs across a study population. This is appropriate for a few samples or several thousand.

General Information

Sample Input

Genomic DNA - Normalized to 5ng/µL

Users must provide their own SNP assays or we can order the assay and bill assay supplies to your project. AZGC does not stock Taqman Assays.

Expected Results

Results table listing the sample genotype detected at each polymorphic site.

Details

Sample Preparation Details

Sample input is gDNA normalized to 5ng/µL. We can receive your samples in 1.5-2.0mL tubes but we prefer 96-well plates. Samples which do not meet our input requirements will be subject to additional handling fees. Please contact our lab if you have questions about sample preparation.

Price

Academic (UA) $5.00 | Academic (non-UA): $6.00 | Industry: $7.50
Unit: Sample well

Contact AZGC to discuss your specific assay reagents.

Turnaround Time

Varies per project

Related Services

DNA Extraction, Quantification, Normalization

AZGC offers a 'Quick and Easy' DNA extraction as a low-cost option for certain sample types.

General Information

Sample Input

We provide you bar-coded tubes with buffer, add your sample and return to AZGC

Expected Results

Genomic DNA suitable for downstream testing in transgenic mouse assays or other robust screening assays.

Details

Sample Preparation Details

For mouse genotyping add 2-4mm of tail tip tissue directly to the buffer in the provided tubes. Seal tightly and return to AZGC.

Workflow

How to get started with your sample submission:

Log into iLab Operations Software and from AZGC's core page click Request Services

Video tutorial for iLab submission

*We will review your project request and select an extraction method prior to sample processing

Samples are taken directly from cell lysis to PCR saving time and resources.

Price

View AZGC Current Pricing

Academic (UA) $2.25 | Academic (non-UA): $2.70 | Industry: $3.38| Unit: Sample

Turnaround Time

2 business days- does not include downstream genotyping

Related Services

Transgenic Mouse Genotyping

Additional Information

This method forgoes certain quantification and purification steps when unnecessary for downstream processing.

AZGC offers a variety of Illumina NextSeq 550 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 NextSeq 500 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
• Exome Sequencing
• RNASeq (transcriptome sequencing)
• Single Cell Sequencing

Expected Results

• Read length - 1x75, 2x75, 2x150
• Average data output:
• 1x75 High Output: 25Gb - 30Gb
• 2x75 Mid Output: 16.25Gb - 19.5Gb
• 2x75 High Output: 50Gb - 60Gb
• 2x150 Mid Output: 32.5Gb - 39Gb
• 2x150 High Output: 100Gb - 120Gb

Data Delivery: 

Data is now returned via BaseSpace Sequence Hub. This platform offers storage and data analysis tools. Register for an account once your sequencing order is complete.

Inquire at azgc@arizona.edu for quote

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
• 10+ µg total DNA for 10kb mate pair libraries
• 10µg total DNA for 3kb and 5kb mate pair libraries

RNA sample requirements:

• 100ng-2µg 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:

• Qubit to verify the quantity of starting material
• Fragment Analyzer to check the material quality

Cluster Generation: Cluster generation requires 10nM post library construction concentration

Sequencing Chemistry: AZGC uses Illumina NextSeq 2-channel SBS chemistry

Library Preparation/Construction: AZGC uses a variety of DNA/RNA library construction kits

*Note: Per Illumina recommendations we cannot run libraries that are more than 6 months old. Therefore, your library material will be disposed of 3 months after they are built in accordance with our SOPS.

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

Price

Academic (UA): $300.00 | Academic(non-UA): $360.00 | Industry: $450.00 | Unit: Per Machine Run

Note- Flow cells are priced separately. Contact AZGC for a quote including Library prep, Sequencing and data analysis.

Turnaround Time

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

Average data turnaround time for most NGS projects is approx. 6-8 weeks.

The AZGC 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 data

Additional Information

If there is a specific application you are interested in on the NextSeq550 but do not see listed here, please contact us to see if we can accommodate your needs.

University Customers: We are located in Keating Building Room 106. Samples may be left in the freezer at the north entrance to our lab. Samples should be clearly labeled "Illumina" along with your iLab Service ID.

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

AZGC offers Illumina MiSeq supported applications including DNASeq, RNAseq, targeted gene sequencing, Metagenomics (16S/custom), small genome sequencing, amplicon sequencing and other NGS pipelines.

General Information

Sample Input

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

Applications include:

• Small Genome Sequencing (Shotgun/de novo)
• Other supported and custom protocols (please inquire)
• Metagenome Analysis (16S/custom)
• CHiPseq
• miRNA profiling
• Methylation Analysis
• Cancer Genomics (RUO)
• RNASeq (transcriptome sequencing/expression analysis)
• Library QC
• Single Cell sequencing

Expected Results

Expected Results: Select from Version 2 (v2) or Version 3 (v3)

v2kits:

• Read length: 1x50SR, 2x25PE, 2x150PE, 2x250PE
• Average data output: 750Mb (1x50SR, 2x25PE), 4.5Gb (2x150PE), 7.5Gb (2x250PE)

v3kits:

• Read length: 2x75PE, 2x300PE
• Average data output: 3.3Gb (2x75PE), 13.2Gb (2x300PE)

Data Delivery: 

Data is now returned via BaseSpace Sequence Hub. This platform offers storage and data analysis tools. Register for an account once your sequencing order is complete.

Details

Sample Preparation Details

DNA Sample Requirements (if not submitting tissue, cells, etc. for extraction):

• 1-3µg total DNA required (shotgun/de novo and Exome sequencing)
• DNA should contain no particulate matter
• 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

RNA Sample Requirements:

• 200ng-4µg total RNA required depending on the application
• RNA should be resuspended in RNase free water and kept at -80°C until delivery to AZGC
• 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

*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 AZGC to discuss further data analysis needs.

Price

Academic (UA): $300.00 | Academic (non-UA): $360.00 | Industry: $450.00 | Unit: Per Machine Run

Note- Flow cells are priced separately. Contact AZGC for a quote including library prep, sequencing and data analysis services.

Turnaround Time

Average turnaround time will vary depending upon the application and sample input. Average data turnaround time for most NGS projects is approximately 6-8 weeks. The AZGC operates on a first come, first serve entry into sample queue.

Related Services

High Recovery DNA Extraction, RNA Extraction and QC (Agilent Bioanalyzer 2100), Sanger DNA sequencing for validation of NGS data

Additional Information

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

University Customers: We are located in Keating Building Rm 106. 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:
Arizona Genetics Core
ATTN: Illumina NGS
1657 E. Helen Street
Keating Building, Rm 106
Tucson, AZ 85721

AZGC offers purification of 96-well PCR products using EdgeBioSystems ExcelaPure PCR purification blocks. ExcelaPure 96-well UFC plates contain an optimized ultrafiltration membrane for high recovery of your PCR products.

General Information

Sample Input

To use this service, submit your templates in a 96-well reaction plate.

Expected Results

PCR product free from excess primers, dimers, DNTPs and salts which can interfere with DNA Sequencing.

Details

Sample Preparation Details

To use this service, submit your templates in a 96-well reaction plate.

The samples will need to be brought up to 100µL with molecular grade water.

To use this service as part of your DNA Sequencing workflow, simply check the radio button for "clean up" in the submission form when you submit your plate for High Volume Sequencing in iLab Operations Software.

Workflow

• Log in to iLab Operations Software and click Request Services.
• Record and attach the numbers at the end of your iLab Service ID to your samples and send or deliver to AZGC.
• Upload your sample information

Excess primers, primer dimers, dNTPs and salts are filtered out under vacuum pressure, while your purified PCR product is retained on the ultrafiltration membrane.

Price

See AZGC current pricing

Academic (UA): $80.00 | Academic (non-UA): $96.00 | Industry: $120.00 Unit: 96-well Plate

Turnaround Time

3 days

Related Services

DNA Sequencing Quantification and Normalization PCR Products

AZGC offers high quality and fast turnaround fully automated DNA sequencing on multiple Applied Biosystems 3730 DNA Analyzers.

General Information

Sample Input

Samples can be submitted for low volume (tubes) or high volume (96-well plates) sequencing.

Accepted sample types include PCR product, plasmid DNA, phage, or BACs, cosmids and single-stranded DNA.

Expected Results

Users of this service can expect up to 600 bases per read.

Data can be downloaded directly from your project in iLab Operations Software.

Details

Sample Preparation Details

Please review our Sequencing FAQ to prepare your submission and template DNA according to the guidelines.

Accepted sample types include PCR product, plasmid DNA, phage, or BACs, cosmids and single-stranded DNA.

Provide your own sequencing primer or use our standard universal primers at no extra charge. 

AZGC Universal Primers

Samples should be eluted in (MilliQ) water. Minimum volume required:
     8µL of template per reaction
     5µL of primer per reaction

Low volume (tube) sequencing should be submitted in 1.5mL snap-cap tubes. Sample and primer must be submitted in separate tubes.
*Note: If you have more than 22 sequencing reactions it will be more cost effective to use the High Volume (plate) sequencing workflow.

High-volume sequencing should be submitted in a 96-well v-bottom plate.

PCR products should be prepared with commercially available PCR cleanup kits and eluted in (MilliQ) water to remove excess primers, nucleotides, and buffers.

Automated sample cleanup, quantification, and normalization service is available for High-volume (96-well plate) sequencing submissions - simply select these options in your iLab project request.

Workflow

Log into the AZGC's iLab landing page and select Request Services.

Video tutorial for High Volume Sequencing Request

*Drop off your sequencing submission in the freezer outside Keating 106, in Life Sciences South Rm 205, or by send to

Users of this service can expect 600 bases or greater per read.

View our Sequencing FAQ page for tips about what can cause messy or degraded sequence data.

Price

Low Volume Single Tube Sequencing-

Academic (UA): $6.25 | Academic (non-UA): $7.50 | Industry: $9.38 | Unit: Reaction

High Volume 96-well Plate Sequencing-

Academic (UA): $195.00 | Academic (non-UA): $234.00 | Industry: $295.50 | Unit: 96-Well Plate

Turnaround Time

2-3 working days

Related Services

Please visit our Pricing page

PCR Clean Up and Quantification (available for whole plate only) for High-Volume Sequencing.

Additional Information

If you are submitting more than 29 samples (or 29 total reactions) it will be cost effective to order High Volume Plate Sequencing. If you have fewer than 29 reactions it will be more cost effective to submit these as separate tubes for Low Volume Sequencing.

AZGC provides a variety of DNA extraction services to fit any project or budget.

We can provide researchers with bar-coded collection tubes. Sample submissions will be uploaded directly through iLab Operations Software.

PCR-ready genomic DNA can either be processed at AZGC or returned in plates or tubes to the researcher.

Our Extraction Services include:
        •  High-throughput DNA Extraction
        •  High-recovery DNA Extraction
        •  Quick and Easy DNA Extraction
        •  RNA Extraction

Trizol Preparation

1. Homogenize tissue with very cold mortar and pestle or homogenizer.
2. Transfer tissue into 1.7mL Eppendorf tube or 25mL Falcon tube.
3. Add 10µL TRIZOL / mg tissue, vortex thoroughly.
4. Run tissue/TRIZOL mixture through a 20 gauge needle several times to complete homogenization.
5. Let stand at room temperature for 5 minutes.
6. Add 20µL chloroform / 100µL TRIZOL, vortex for 15 seconds, and leave at room temperature for 3 minutes.
7. Centrifuge samples at maximum rpm for 15 minutes at 4°C.
8. Transfer aqueous phase to a fresh tube (the use of Eppendorf PhaseLock Gel greatly decreases organic phase contamination at this step).
9. Add 50µL isopropyl alcohol / 100µL TRIZOL and incubate at room temperature for 10 minutes.
10. Centrifuge samples at maximum rpm for 10 minutes at 4°C.
11. Remove supernatant.
12. Wash RNA pellet with 80% ethanol and vortex.
13. Centrifuge samples at 7,500g for 5 minutes at 4°C.
14. Remove supernatant.
15. Reconstitute pellet in 20µL of RNase free water.

Lysis Buffer

• 50 mM Tris pH 8.0
• 50 mM EDTA
• 25 mM Sucrose
• 100 mM NaCl
• 1% SDS

Low TE pH 8.0

• 10 mM Tris pH 8.0
• 0.1 mM EDTA pH 8.0

RNAlater™

• 25 mM Sodium Citrate
• 10 mM EDTA
• 70 g ammonium sulfate/100 ml solution, pH 5.2

(Information taken from patent information: US Patent 6,204,375)

Ribotyping (C.diff) Protocol

AZGC offers ribotyping via capillary electrophoresis. The primers and protocol we use is per the protocol described by 
Indra A, Huhulescu S, Schneeweis M, Hasenberger P, Kernbichler S, Fiedler A, Wewalka G, Allerberger F, Kuijper E. J. Med. Microbiol. 57(11):1377-1382 doi:10.1099/jmm.0.47714-0

 characterization of clostridium difficile isolates using capillary electrophoresis based pcr ribotyping full pdf

10X Genomics Visium Assay

AZGC offers spatial transcriptomics powered by the 10X Visium Assay. Slides with pre-set capture areas (6.5mm x 6.5mm) each containing 5000 barcoded spots allows for near single cell whole transcriptome analysis.  This workflow allows to analyze  gene expression of cells with the context of the tissue morphology.

Image

10x Visium - Spatial Gene Expression

Together with the Microscopy core, we provide full service, imaging and spatial gene expression workflow and sequencing. For more details about 10x Genomics Visium Spatial Gene Expression see: https://www.10xgenomics.com/products/spatial-gene-expression

Note- For a new tissue types, a tissue optimization must be performed prior to testing your sample materials. AZGC can assist with the planning of your experiment.

Please contact: AZGC (azgc@arizona.edu) in order to discuss & plan for Visium Spatial Gene Expression projects.