Microbiome/Amplicon Service

Contact for Genomics and Bioinformatics Consultation

Email Dr. Magdy Alabady at malabady@uga.edu for a consultation on new or existing Genomics and Bioinformatics projects. Also, you can contact Dr. Alabady for assistance with grant proposals and for obtaining a letter of support from GGBC.

Contact for Microbiome Technical Assistance

For technical questions about existing or new Illumina projects, please contact the following Genomics Professional;

• Kateryna Stoianova (kstoianova@uga.edu)

More contacts

Please visit our “All Inquiries” page for detailed information about who you should contact at GGBC to receive a quick and accurate response.

As of April 1^st, 2022, GGBC implemented the following changes to the Microbiome Amplicon Sequencing Workflow in order to make the greatest use of our time and resources at GGBC to assist the larger genomic community at UGA and beyond.

1. Researchers must amplify the target regions (16S/18S/ITS/etc.) in their laboratories utilizing their specific primers. The specific primers must have overhangs (universal sequence added to the 5’ end of the specific primers to create binding sites for the barcoded primers in the 2^nd PCR step) as follows:

5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-Forward-Specific-Primer-Sequence 3’

5’ GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-Reverse-Specific-Primer-Sequence 3’

We have several sets of primers in the lab and are willing to provide aliquots to people who wish to test things out in their own labs.

2. Researchers must give evidence of an acceptable target region amplification and the lack of secondary PCR products. This can be a good-resolution gel image or bioanalyzer DNA or fragment analyzer NGS traces. The latter two can be done at GGBC for a fee.

3. Researchers are encouraged to use beads or columns to separate the specific target amplificons from free primers and nucleotides. If they can’t do this step in their laboratories, it can be done at GGBC.

4. Researchers must submit at least 15 µl of the amplicon products in a 96-well v-bottom plates.

With these modifications, the New Microbiome Amplicon Sequencing Workflow will include the following steps:

1. Clean the initial PCR product provided by the researcher, if necessary.

2. Check the concentration with the Synergy HT plate reader.

3. Performing the second PCR to add the barcoded Illumina adapters to all samples.

4. Clean the second PCR products using Ampure Beads.

5. Determine the concentration using the Synergy HT plate reader.

6. Assess a randomly selected set of samples to determine the size of the library using the Fragment Analyzer.

7. Pooling the barcoded libraries using equimolar ratio.

8. Determine the size of the pooled library using the Fragment Analyzer.

9. Clean the pool with Ampur beads if necessary.

10. Determine the pool concentration using Qubit and qPCR.

11. Sequencing.

 

*Under special circumstances we will accept projects that need to be started from gDNA and taken through the PCR1 target region amplification. Please contact us for further information.

As we get more information or new primers, the table will be updated.

Contact for Financial Inquiries and Quote Requests

Please email Kim and Elizabeth at ggbc@uga.edu, for financial inquiries or to request a quote. Be as specific as possible, so that they can more quickly assist you.

Table 1. Illumina compatible library preparation fees

llumina Compatible Library Type (submitted in 96 well plate)	UGA Fee	Non-UGA Fee	Commercial Fee
Amplicon specific primers with overhang (if necessary)	$150.00	$177.00	$188.00
DNA/PCR product clean up (per half plate)	$98.00	$116.00	$123.00
DNA/PCR product clean up (per plate)	$191.00	$226.00	$239.00
Modified Amplicons (16S/ITS/Custom)(up to 48 samples per plate)	$457.00	$540.00	$572.00
Modified Amplicons (16S/ITS/Custom)(49 to 96 samples per plate)	$681.00	$804.00	$852.00

Table 2. Library pooling and pre-sequencing QC fees

Service Description	UGA Fee	Non-UGA Fee	Commercial Fee
Library Pooling up to 2-24 samples	$60	$71	$75
Library Pooling up to 25-48 samples	$105	$124	$132
Library Pooling up to 49-96 samples	$162	$192	$203
Library Pooling up to 97-144 samples	$234	$277	$293
Library Pooling up to 145-192 samples	$306	$362	$383
Library Pooling up to 193-288 samples	$436	$515	$545
Library Pooling up to 289-384 samples	$565	$667	$707
Pre-Sequencing QC (Qubit, FA, Kapa)	$120	$142	$150

Table 3. Illumina run types

Run Type	Expected number of reads passing filter (million)a	Expected total number of basesa	UGA Fee	Non-UGA Fee	Commercial Fee
MiSeq (500 Cycles) (v2) flow cell; PE250	24-30	7.5-8.5 Gb	$1,932	$2,280	$2,415
NextSeq2000 (600 Cycles) flow cell (P1); PE300	200	60 Gb	$2,493	$2,942	$3,117
NextSeq2000 (600 Cycles) flow cell (P2); PE300	600	180 Gb	$4,709	$5,557	$5,887