We are conveniently located within the Krajmalnik-Brown laboratory, in the Biodesign Swette Center for Environmental Biotechnology. We offer genomic-based analyses including next-generation sequencing – using Illumina® MiSeq and HiSeq sequencing platforms for the microbiome studies in collaboration with Genomics Core at Biodesign. Both teams are fully trained on Illumina® sequencing and the latest bioinformatics software for data processing.
Since we started in summer 2014, we have received requests from over 30 labs at ASU, UofA , NAU and institutions across the US, Spain, Mexico and South Korea. We've processed more than 3,000 samples and more than 1,000 DNA extractions so far, bringing us to 30 Illumina sequencing libraries for 16S and 1 for ITS (fungi).
Who are we?
Rosa Krajmalnik-Brown is an Associate Professor at the School of Sustainable Engineering and The Built Environment and the BSCEB and Director of the Microbiome Analysis Lab.
Juan Maldonado is an Assistant Research Scientist at BSCEB and Manager of the Microbiome Analysis Lab.
Morgan Bennett is a Research Specialist at BSCEB and Microbiome Analysis Lab.
Carole Flores is the Business Operation Manager at BSCEB and Microbiome Analysis Lab.
What do we offer?
- Illumina® Amplicon Sequencing: Available for bacteria/archaea (16S) and fungi (ITS1)
- DNA extraction: Available for small sample sets and high-throughput
- Bioinformatic Analysis: Process sequencing data and provide comprehensive report
- Transcriptomics: RNA-Seq analysis
- Terminal Restriction Fragment Length Polymorphism (TRFLP): Fingerprinting method for microbial communities
- Quantitative PCR (qPCR): Quantification of specific genes of interest
What is our general workflow for Illumina Amplicon Sequencing?
The first step is to contact us, in person at Biodesign Institute, by phone at (480) 965-7495 or by email (firstname.lastname@example.org). We will make sure we can provide the appropriate services for your project. Also, we can provide you a quote estimate or a support letter for your future projects.
This is a very critical and important step for microbiome analysis. Ship samples in a cooler with ice packs or dry ice. That will help to keep your samples/DNA stable. If you are shipping DNA or raw samples (soil, stool, culture…) please confirm that you are complying with the shipping regulations. Also, ship the your samples with enough time so they arrive at the lab by Friday (and not during the weekend). You can also deliver the samples in person to us at Biodesign Institute.
We extract DNA from many types of biological samples (ex. soil, fecal matter). The initial step of the extraction is done in a biosafety cabinet in our clean room to reduce contamination risk. We then transfer the samples to a high-throughput (HTP) format and use the epMotion robot for the remaining steps of the extraction.
Once we have extracted the DNA, we use the Nanodrop to check the quantity and quality of the DNA.
We prepare the PCR reactions using the epMotion robot. We offer two types of barcoded primers. Bacteria (16S) and Fungi (ITS). At this step, each sample is assigned a unique barcode that will later be used during data analysis. Samples are run in triplicate reactions.
We use agarose gel electrophoresis to check for amplification of each sample and its amplicon size. This indicates the success of the PCR reaction.
To quantify the amount of DNA in each sample, we use a Picogreen assay. Picogreen is a fluorescent probe that binds to double-stranded DNA. Values are read using the plate reader.
When we pool all of the samples for a library, each sample is added at the same concentration. We use the concentration values from the Picogreen assay to calculate what volume of each sample to pool. The epMotion robot is programmed to transfer the specific amount for each sample.
Purify & Quantify Library
After pooling all the samples together, we purify the library before using qPCR to check its concentration.
Once the library is quantified we submit it to our partners at the Core Genomics laboratory at Biodesign.
Data Analysis & Data Return
Once the data is back from the sequencer. We will provide you a single file in a .fastq format with all sequences from all you samples and a mapping file with your samples identifiers.
We will send you a link to ASU Dropbox, where your data will be available just for you.
As an extra service we can provide you curated analysis of your data by using several bioinformatic tools including QIIME.
Along with the data we will send you the invoice of the service. Carole Flores will help you with the payment.