Arizona Genetics Core offers Single Cell Sequencing using the 10x Genomics Chromium Controller.

Arizona Genetics Core offers single cell RNA sequencing using the 10xGenomics Chromium Controller. This workflow uses uniquely barcoded “Gel Bead-in-emulsion” (GEMs) to individually capture single cells or nuclei for downstream single cell gene expression, immune profiling, and/or ATAC library preparation. 

General Information

Sample Input

Freshly collected cells should be provided as single cell suspensions following the recommended guidelines for sample preparation from 10x Genomics

Single Cell 3’ Gene Expression / Single Cell Immune Profiling

500 -10,000 fresh Cells in single cell suspension (Concentration: ~700 - 1,200 cells/uL, >90% Viability)

Single Cell ATAC + Gene Expression

500 - 10,000 fresh Nuclei in single nuclei suspension (Concentration: ~400 - 8,000 nuclei/uL)

10x Visium - Spatial Gene Expression

AZGC also offers spatial gene expression services using 10x Genomics Visium slides. 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

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

Workflow

Please contact AZGC (azgc@arizona.edu) at least 1 month prior to the anticipated sample submission, in order to work together to best set up your project and ensure we have the necessary reagents available for your single cell sequencing needs.

Price

Academic (UA): please inquire | Academic (non-UA): please inquire | Industry: please inquire
Unit: Project

Turnaround Time

please contact us to discuss

Additional Information

https://www.10xgenomics.com/

This extraction method is ideal for samples with a limited amount of source material or a low expected yield. This process can also be used to extract high quantity, high molecular weight DNA for intensive downstream testing such as Exome Sequencing.

General Information

Sample Input

The Arizona Genetics Core accepts a variety of sample types suitable for this process, including buccal swabs, blood, plant tissue, and cell pellets.

Expected Results

High Quality Genomic DNA, quantified and returned in tubes.

Details

Sample Preparation Details

Please contact the lab to discuss your sample type and the necessary preparation for this extraction.

Workflow

How to get started with your sample submission:

Log into iLab Operations Software and from Arizona Genetics Core's core page click Request Services

View Video tutorial for iLab submission

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

Overnight cell lysis precedes DNA extraction by Phenol Chloroform or other High Recovery protocol.

Genomic DNA will be resuspended in our LowTE buffer unless otherwise requested.

Price

Academic (UA): $22.00 | Academic (non-UA): $26.40 | Industry: $33.00 | Unit: Sample

See Current Pricing

Turnaround Time

Varies by project

Related Services

Genotyping

Additional Information

This process is also available for FFPE preserved tissues as well as blood samples. Please contact core staff to see if our high-recovery extraction is right for you.

Quality RNA isolation is often the first step to a successful gene expression or transcriptome project.

General Information

Sample Input

AZGC offers RNA isolation from most tissue types, including blood or cell cultures. We can provide collection tubes containing RNA later.

Expected Results

Quality and quantity of isolated RNA is assessed using our 2100 Bioanalyzer from Agilent Technologies (additonal QC charges apply).

Details

Sample Preparation Details

Tissue should be stored in RNAlater immediately upon collection.
Cells may be stored frozen.
Contact Core staff to discuss your sample preparation needs for RNA isolation

Workflow

How to get started with your sample submission:

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

View Video tutorial for iLab submission

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

We extract RNA using Qiagen RNAeasy Mini Kit- other kits and protocols are available upon request.

Tissue should be stored in RNAlater immediately upon collection.

Following extraction, RNA quality is assessed on our Agilent 2100 Bioanalyzer.

Price

View AZGC Current Pricing

Academic (UA): $36.00 | Academic (non-UA): $43.20 | Industry: $54.00 | Unit: Sample

Turnaround Time

Varies by project

Related Services

Agilent Technologies 2100 Bioanalyzer for sample QC

Additional Information

All plasticware used should be certified as RNAse free. Handle your sample with gloves on to avoid contamination.

The Arizona Genetics Core offers a variety of Next-Gen Sequencing 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 submitted to our core.  We also offer DNA or RNA extraction for library prep.

Applications include:

• Whole Genome Sequencing (Shotgun/de novo)
• Metagenome Analysis
• CHiPseq
• miRNA profiling
• Exome Sequencing
• RNASeq (transcriptome sequencing)
• Single Cell Sequencing
• Other supported and custom protocols (please inquire)

Expected Results

• Data output available from Element AVITI, Illumina Miseq, NextSeq550 or NovaSeq Platforms
• Trimming, demultiplexing and quality filtering is included at no additional charge

Data Delivery: 

Data is now returned via Cyverse. 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-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:

• 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

Library Preparation/Construction: Arizona Genetics Core uses a variety of DNA/RNA library construction kits

*Note: Per kit 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 Arizona Genetics Core to discuss further data analysis needs.

Price

Contact Arizona Genetics Core 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. 6-8weeks.

Arizona Genetics Core operates on a first come, first serve entry into sample processing queue.

Related Services

High Recovery DNA Extraction

RNA Extraction and analysis (Agilent Bioanalyzer 2100)

Sanger DNA sequencing for validation of NGS data

Additional Information

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 "NGS" 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 St.
Keating Building, Rm 106
Tucson, AZ 85721

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 of high quality Phred scores 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. 

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 29 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 sending to

Users of this service can expect 600 bases or greater of high quality Phred scores 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: $292.50 | 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 30 samples (or 30 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.