1352856131117_a2336ed1c2cc707a7d464a3906810725

Microbiome Core Facility

Chapel Hill, North Carolina

The human body is the home to approximately 10,000,000,000 bacterial cells that inhabit our gastrointestinal tract, mouth, urogenital tract, and our skin. Most of these bacteria are uncultivable, which meant in the past that researchers were unable to study and characterize them. The development of metagenomic technologies allow us today to examine microbial communities through culture independent techniques, of which the most used are next-generation sequencing methods.

The UNC Microbiome Core Facility was established to provide technical and research support to study community structure and function of host-associated microbial populations.

    16S Phylogenetic Studies
    $64.00 USD
    per Hour

    Bioinformatics analysis of 16S amplicon sequencing data

    UNC/NC State or covered by federal funds $64
    non UNC/NC State or not covered by federal funds $68

    Bioinformatics analysis of 16S amplicon sequencing data

    UNC/NC State or covered by federal funds $64
    non UNC/NC State or not covered by federal funds $68

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    Genomic DNA extraction
    $16.00 USD
    per Sample

    Isolation of total DNA.

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

    Isolation of total DNA.

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

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    Illumina NGS
    Illumina next generation sequencing
    $823.00 USD
    per Lane

    Illumina sequencing
    MiSeq SE5(50) $823 $1,193
    MiSeq PE150(300) $1023 $1,483
    MiSeq PE250(500) $1125 $1,631
    MiSeq PE300(600) $1478 $2,143
    HiSeq High output SE50 $913 $1,324
    HiSeq High output PE50 $1503 $2,179
    HiSeq High output SE100 $1238 $1,795
    HiSeq High output... Show more »

    Illumina sequencing
    MiSeq SE5(50) $823 $1,193
    MiSeq PE150(300) $1023 $1,483
    MiSeq PE250(500) $1125 $1,631
    MiSeq PE300(600) $1478 $2,143
    HiSeq High output SE50 $913 $1,324
    HiSeq High output PE50 $1503 $2,179
    HiSeq High output SE100 $1238 $1,795
    HiSeq High output PE100 $2153 $3,122
    HiSeq RAPIDSE50 $1073 $1,556
    HiSeq RAPIDPE50 $1827 $2,649
    HiSeq RAPIDSE100 $1561 $2,263
    HiSeq RAPIDPE100 $2802 $4,063
    HiSeq RAPIDPE150 $3265 $4,734

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    Ion Torrent NGS
    Ion Torrent next generation sequencing
    $767.00 USD
    per Chip

    The Ion Torrent sequencing platform from Life Technologies employs First PostLight™ sequencing technology (semiconductor technology). The detection of a specific nucleotide on a growing DNA strand occurs inside a well of an Ion Torrent semiconductor chip. The incorporation of the correct base triggers a chemical reaction that releases... Show more »

    The Ion Torrent sequencing platform from Life Technologies employs First PostLight™ sequencing technology (semiconductor technology). The detection of a specific nucleotide on a growing DNA strand occurs inside a well of an Ion Torrent semiconductor chip. The incorporation of the correct base triggers a chemical reaction that releases a hydrogen ion as byproduct, which in turn changes the pH of the solution. The Ion sensor captures voltage change measurements from the direct release of hydrogen ions following DNA polymerization and incorporation events get recorded as digital signals 1 and 0. This technology differs from other sequencing technologies in that no modified nucleotides, no lasers, no optics, no camera, no fluorescence, no enzyme cascade are used.

    Ion Torrent sequencing fees:

    314 (400bp read)
    UNC/NC State/ Covered by federal funds $767
    Non-UNC or NC State or not covered by federal funds $1,212

    316 (400 bp read)
    UNC/NC State/ Covered by federal funds $1,057
    Non-UNC or NC State or not covered by federal funds $1,607

    318 (400 bp read)
    UNC/NC State/ Covered by federal funds $1,464
    Non-UNC or NC State or not covered by federal funds $2,225

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    Molecular cloning
    $162.00 USD
    per Run

    Clone library creation:
    In order to confirm bacterial identity, PCR-amplified 16S rDNA fragments can be cloned into plasmids and transformed into an appropriate host (usually E. coli). Each transformed E. coli colony will contain only one 16S rDNA PCR-originated fragment from the original sample. A number of colonies are picked... Show more »

    Clone library creation:
    In order to confirm bacterial identity, PCR-amplified 16S rDNA fragments can be cloned into plasmids and transformed into an appropriate host (usually E. coli). Each transformed E. coli colony will contain only one 16S rDNA PCR-originated fragment from the original sample. A number of colonies are picked randomly and the insert is sequenced. The DNA sequence is then compared to a database (for example RDP II) for identification by DNA homology.

    Equipment:
    Genetix QPix2 XT Colony Picker System

    UNC/NC State/ Covered by federal funds $480
    Non-UNC or NC State or not covered by federal funds $528

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    Plasmid DNA extraction
    $16.00 USD
    per Sample

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

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    RNA extraction
    $16.00 USD
    per Sample

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

    UNC/NC State/ Covered by federal funds $16
    Non-UNC or NC State or not covered by federal funds $25

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    RNA sequencing
    $220.00 USD
    per Sample

    - Illumina RNA Library preparation with barcoding

    UNC/NC State/ Covered by federal funds $220
    Non-UNC or NC State or not covered by federal funds $319

    - Illumina RNA Library preparation with barcoding

    UNC/NC State/ Covered by federal funds $220
    Non-UNC or NC State or not covered by federal funds $319

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    Roche 454 NGS
    Roche 454 next generation sequencing
    $9,797.00 USD
    per Plate

    Pyrosequencing is a DNA sequencing technique that utilizes enzyme coupled reactions and bioluminescence to monitor the pyrophosphate release accompanying nucleotide incorporation, in real time. The pyrosequencing method was developed by the group of Pal Nyren. With the aim of commercializing the new DNA sequencing technique, Nyren and... Show more »

    Pyrosequencing is a DNA sequencing technique that utilizes enzyme coupled reactions and bioluminescence to monitor the pyrophosphate release accompanying nucleotide incorporation, in real time. The pyrosequencing method was developed by the group of Pal Nyren. With the aim of commercializing the new DNA sequencing technique, Nyren and others founded Pyrosequencing AB in 1997. The technology was licensed to 454 Life Sciences, which was later acquired by Roche in 2007. 16S DNA amplicon sequencing enables the identification and quantification of bacteria within complex mixtures of PCR amplicons.

    454 amplicon pyrosequencing fees:

    Full plate
    UNC/NC State/ Covered by federal funds $9,797
    Non-UNC or NC State or not covered by federal funds $10,758

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    TRFLP
    Terminal restriction fragment length polymorphism
    $130.00 USD
    per Sample

    TRFLP is a method that allows the identification of major phylogenetic groups in complex microbial communities. It is based on the treatment with restriction enzymes of a DNA fragment specifically amplified by PCR. The terminal fluorescent-labeled fragments produced are separated by size using a DNA sequencer. Each specific bacterial... Show more »

    TRFLP is a method that allows the identification of major phylogenetic groups in complex microbial communities. It is based on the treatment with restriction enzymes of a DNA fragment specifically amplified by PCR. The terminal fluorescent-labeled fragments produced are separated by size using a DNA sequencer. Each specific bacterial group will produce a specific profile that can be identified by comparing them to existing profile databases.

    UNC/NC State/ Covered by federal funds $130
    Non-UNC or NC State or not covered by federal funds $150

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    qPCR
    Quantitative PCR
    $21.00 USD
    per Sample

    The method is based on the conserved 16S rDNA gene present in all bacteria (a comprehensive list of 16S rDNA sequences from gut bacteria have been deposited and categorized in the Ribosomal Database Project II ). By calculating the number of conserved 16S rDNA genes, qPCR can indirectly indicate the number of bacteria present in a... Show more »

    The method is based on the conserved 16S rDNA gene present in all bacteria (a comprehensive list of 16S rDNA sequences from gut bacteria have been deposited and categorized in the Ribosomal Database Project II ). By calculating the number of conserved 16S rDNA genes, qPCR can indirectly indicate the number of bacteria present in a given sample. Additionally, appropriate design of qPCR oligonucleotide probes (primers) that can identify the sequence of the 16S gene variable regions allows for the amplification of genes from a specific bacterium of interest whilst excluding all other bacteria, making qPCR a useful tool for quantifying specific bacteria in a complex microbial community.
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    Fees:

    - qPCR one-time set up fee
    UNC/NC State/ Covered by federal funds $118
    Non-UNC or NC State or not covered by federal funds $169

    - qPCR
    UNC/NC State/ Covered by federal funds $21
    Non-UNC or NC State or not covered by federal funds $28

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Jesse vanWestrienen gave a positive review for Plasmid DNA extraction:

January 27, 2014
M. Andrea was great to work with. She was extremely accommodating expanding the scope of the project and rushing the deliverable due to a tight deadline on my end. Most importantly the data is clean and samples secure.

Desmond Mascarenhas gave a positive review for qPCR:

January 07, 2013
Great job! Thanks.

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