Functional Genomics Services
Services and Equipment
Agilent Fragment Analyzer
The 96 capillary fragment analyzer is ideal for large sample size analysis for RNA quality, NGS libraries or PCR products. Kits available:
Standard and High Sensitivity RNA
Standard and High Sensitivity NGS DNA
High Molecular Weight Genomic DNA
More information about additional options is available at
https://www.agilent.com/search/?Ntt=Fragment%20Analyzer
For additional information and pricing contact Surabhi Sonam (sonam2@illinois.edu) or Mark Band (markband@illinois.edu).
Standard Biotools Genomics Systems
Up to 9216 qPCR or SNP analysis reactions may be performed simultaneously using the Biomark HD high throughput amplification system. Targeted resequencing can be performed on the Access Array Integrated Fluidic Circuit (IPC) on the Juno, producing up to 48 tagged sample amplicon libraries using up to 48 primer pairs, ready for Illumina i100 or NovaSeq sequencing. Microbiome community sequencing can be carried out with 16S, ITS, Archaea and functional gene primers simultaneously.
Contact us to discuss your projects.
Download the Access Array submission form here.
Illumina iScan
Image of a single bead cluster showing genotypes for one DNA sample.
SNP genotypes: AA (green), BB (red), AB (yellow)Analysis of bead array signals is carried out using the Illumina GenomeStudio software.
Genotype calls are exported in tabular format compatible for linkage or association studies with third party programs.
SNP cluster showing genotype calls for 96 DNA samples.
For additional information and specific project pricing contact Dr. Mark Band (markband@illinois.edu)217-244-3930.
All work performed by the Roy J. Carver Biotechnology Center (CBC) should be acknowledged in scholarly publications, posters, and presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any CBC personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author.
The Functional Genomics Laboratory is equipped with an Illumina iScan for SNP genotyping and Human Methylation arrays. Illumina arrays are based on oligo coated beads each unique to a specific SNP locus. The beads are randomly distributed and located in 3 micron wells etched in a slide.
Beadarrays include all commercially available Illumina Arrays as well as Agricultural Consortium Arrays. https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
For a full list of available products or an overview of the beadarray technology see the Illumina website at http://www.illumina.com/. Custom SNP design is also available through Illumina.
Hybridized high density Infinium slides are scanned in the Illumina iScan
Real Time PCR QuantStudio 7
We strongly suggest reading the following technical bulletins published by Applied Biosystems explaining the principles of Real-Time PCR before planning your assays.
- **New** Real Time PCR User Instructions
- Designing MGB Probes and Primers
- Essentials of realtime PCR
- Guide to relative quantitation
- Rapid Assay developement guidelines
- Real time vs. traditional PCR
- User bulletin 2
For more information contact Dr. Mark Band at the Functional Genomics Lab. Tel: (217)244-3930
E-mail: markband@illinois.edu
All work performed by the Roy J. Carver Biotechnology Center (CBC) should be acknowledged in scholarly publications, posters, and presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any CBC personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author.
The QuantStudio 7 real time PCR machine is available for use by all university researchers. The use of low volume reactions and 384 well plates conserves both reagents and budget. In addition, our machine is equipped with an autoloading robot allowing 24 hour use of the machine. Real time PCR is one of the most sensitive and accurate assays for RNA expression analysis, allele discrimination or DNA quantification. Users are trained for sample setup and analysis by Functional Genomics Lab staff. Users prepare their samples independently and bring in their PCR plates ready to run. Sequence Analysis software can be downloaded from the Thermo Fisher website. Please contact Tatsiana Akraiko (akraiko@illinois.edu) to set up a training session.
Please provide an account number when making an appointment to use the machine.
| QuantStudio Consumables List Note that barcoded plates are required for plate identification with the autoloader system. | |
| ABI 384 well plates: | 384-Well Clear Optical Reaction Plate (with Barcode, code 128) |
| Part Number 4309849 | |
| 50 plates/box | |
| Optical Adhesive Cover Starter Kit | Part Number 4313663 |
| 20 adhesive covers | |
| 1 compression pad | |
| 1 Cover Applicator | |
| ABI PRISM Optical Adhesive Covers | Part Number: 4311971 |
| 100 Covers/box | |
| ABI SYBER Green Mastermix | Part Number: 4309155 |
| 5 ml. | |
Nucleic Acid Quantification
Qubit
- Accurate at very low concentrations
- Measures only the nucleic acids in a sample and is specific for RNA or DNA
- Does not provide 260/280 or 260/230 ratios
Accurately determining the concentration of your samples is vital for many downstream applications. We offer both a Nanodrop 1000 Spectrophotometer and a Qubit 2.0 Fluorometer for general usage.
The normal turnaround time is 1-2 business days
Qubit uses an intercalating dye and gives more accurate results, especially at lower concentrations.
Nanodrop will measure all nucleic acids so will give accurate results only to very clean samples.
Nanodrop
- Accurate at higher concentrations (above 30ng/ul)
- May take contaminants into account when quantitating nucleic acid and does not differentiate between RNA and DNA
- Provides 260/230 and 260/280 ratios
While these instruments will allow you to measure the quantity and purity of nucleic acid or protein, they will not give data on the quality of each sample. For that, please refer to the Fragment Analyzer page
Forms:
Qubit Submissions:
- We recommend samples be submitted in individual tubes, with each tube labeled with sample name and PI’s initials.
- Submission form must be completed and dropped off with samples OR sent by email (see contacts). If you are submitting the form by email, please have your PI send an email confirming the account number.
- Please contact the lab before bringing your samples so we can ensure that they are placed immediately into the
- 80C freezer.
- Samples must be brought to the lab on ice.
Amplicon Sequencing
We offer both short read with the Illumina platform and long read amplicon sequencing with the PacBio Revio sequencing technologies. Our stock primer sets include multiple 16S short region primers such as V4, V3-V4, V1-V3, V3-V5. Primers for fungal sequencing of the ITS1 and ITS2 region include ITS1F-ITS2, ITS3-ITS4 and ITS7-ITS4. Long read primer sets for full length PacBio amplicon sequencing such as 16S-27F and 16S-1472R and Fungal ITS1F-LR6 can give much higher taxonomic resolution. We also carry many primer sets COI species classification and genes involved in the nitrogen cycle such as nifH, nirK, nirS, nosZ, nrf, amoA and many others. With a set of over 700 primer sets in stock chances are we already have what you are looking for to carry out your next project. Contact us to discuss you next project.
