Services and Request Forms

To request services, please complete the request form by clicking on the appropriate links below. The completed request form should be submitted along with the RNA/DNA samples and microarrays.

     

    Determination of RNA and DNA Quality and Concentration

    It is important to ensure the quality and concentration of the RNA and DNA being submitted for analysis so that money is not wasted for analysis doomed to failure because of the low quality of the sample. The Genomics Core uses a Nanodrop Spectrophotometer and Qubit 2000 Fluorometer to determine concentration. The size and integrity of your sample is determined using electrophoresis on either an Agilent Bioanalyzer 2100 or Agilent 2200 TapeStation. An example of the data provided by the TapeStation can be seen here - See example of results.

      • Concentration measurement by NanoDrop:

      RNA/DNA detected by NanoDrop Spectrophotometer is determined according to the absorbance on A260. The contamination from protein and other organic chemicals in samples can also be detected by absorbance of A280 and A230.  The measurable concentration range is 5ng/μl to 250 ng/μl. High concentration samples should be diluted. The concentration <5ng/μl is not accurate by NanoDrop measurement.

      Print, fill the request form, and submit form with samples

      • dsDNA concentration measurement by Qubit:

      The dsDNA detected by Qubit Fluorometer is determined by measuring the fluorescence dye, which particularly bind to dsDNA. The measurable concentration range by Qubit BR assay kit is 2 ng/μl to 1000 ng/μl. The measurable concentration range by Qubit HS assay kit is 0.2 ng/μl to 100 ng/μl.

      Print, fill the request form, and submit with samples

      • DNA and RNA quality check by Bioanalyzer or TapeStation:

      Always submit your DNA and RNA samples by using the NAase free 0.2 ml PCR tubes or 8x strips or tightly sealed 96 well v-bottom plate (only for TapeStation).  Print, fill the RNA QC request form, or DNA QC request form, and submit with samples.

        Microarrays

        Microarrays provide a relatively fast and money saving way to analyze changes in gene expression and gene dosage. The methodology is robust and the analysis is more straight forward than RNA-seq. This method may be all that you need to generate a list of genes, for further exploration, that change expression under given conditions or caused by disease.

        • Purchase Agilent microarrays:

        You can directly purchase Agilent microarrays from UNC ePro and bring them with your samples and request form to Genomics Core Facility after you received them.

        You can email (yshi@med.unc.edu) a request for order Agilent microarrays by provide following information: PI's name, grant #, your name, your phone#, catalog#, brief description, quantity. We will notice you after we received them.

        • Analysis of mRNA Expression:

        The gene expression microarrays from Agilent are printed as 4 or 8 identical arrays on 1 slide. Plan your experiments with 4 or 8 samples to avoid wasting arrays.

        0.5 µg of total RNA should be submitted in 5 µl volume. All samples and reference RNAs should have the same concentration.

        1 color label method: cDNAs are labeled (amplification) with Cy3-CTP and hybridized on each microarray.

        Print and complete the request form and submit form with samples and microarrays.

        2 color label method: Labeling (amplification) with Cy3- and Cy5-labeled CTP in separate reactions to produce differentially labeled sample and reference cDNAs. Both are hybridized to the same microarray.

        Print and complete the request form and submit form with samples and microarrays.

        • Analysis of Small RNAs:

        The microRNA microarrays from Agilent are printed as 8 identical microarrays on 1 slide. Plan your experiments with 8 samples to avoid wasting arrays.

        The RNA is dephosphorylated and labeled with Cy-dye (Cy3-pCp) for total RNA or small RNA samples.

        The amount of initial RNA is strongly depended on the samples sources and RNA type.

        100 to 400 ng of total RNA should be submitted in a 4 µl volume. All samples should have the same concentration.

        Print and complete the request form; submit form with samples and microarrays.

        • Analysis of Gene Dosage Using Comparative Genomic Hybridization (CGH):

        CGH enables medium to high resolution of changes in copy number across the genome. The data is relatively straight forward to interpret.

        This method uses 2-color direct labeling with Cy-Dye (Cy3 and Cy5) for sample genomic DNA vs reference genomic DNA; both labeled sample DNA and reference DNA hybridize on a same Agilent high density microarrays;

        3 µg of genomic DNA sample and 3 µg of genomic DNA reference are required each in 20 µl volume.

        If you use 4 array (4x) chips, plan your experiments with 4 samples to avoid wasting arrays

        Print and complete the request form; submit form with samples and microarrays

        RNA libraries for High Throughput DNA Sequencing

        While more expensive and more time consuming to analyze, mRNA-seq has the advantage of providing the sequence of the RNAs being studied, in addition to providing relative expression data. The advantages of sequence data include information about possible mutations, gene fusions, and changes in mRNA splicing.

        • mRNA Library

        Prepare mRNA library for high throughput sequence analysis.

        For each sample, 1-2 µg total RNA (20-30 µl) is required. Automation application will depend on number of samples.

        Print and complete the request form and submit form with samples.

        • Small RNA Library

        Prepare small RNA library using Illumina TruSeq small RNA library prep kit.

        For each sample, 1.5-3 µg total RNA in 5 µl volume is required.

        Print and complete the request form and submit form with samples.

        • Total RNA Library

        Prepare total RNA library with Illumina TruSeq Stranded Total RNA Sample prep kit with the Ribo-Zero Gold, which is optimized for removal of both cytoplasmic and mitochondrial ribosomal RNA.

        Get precise measurement of mRNA strand orientation for detection of antisense transcription, enhanced transcript annotation, and increased alignment efficiency. High coverage uniformity enhances the discovery of features such as alternative transcripts, gene fusions, and allele-specific expression.

        The libraries can be made from both high quality, low quality, and degraded (FFPE) RNA samples. For each sample, 0.5-1 µg total RNA in a 10 µl volume is required.

        Print and complete the request form and submit form with samples

          Sample Submission


          • To transfer microarrays:

            Please call or email the Genomics Core to schedule.

             

            • To submit RNA/DNA samples for concentration measurement, quality analysis, microarray analysis, and library preparation:

              Our -80C freezer is located in the basement of LCCC (take the elevator near the loading dock and go down to basement).

              Place the RNA/DNA samples and filled small form in a box in our -80C freezer (see photos below). Place your request forms in the blue bag on the front door of -80C freezer.

              Samples are transferred from LCCC to Carolina Crossing twice per week (Schedule on the front of -80C freezer).

              For samples that require faster processing, please send them directly to our lab at Carolina Crossing Building C, 2234 Nelson Highway, Chapel Hill, NC 27517 (See location map)

               

               

              LCCC Genomics Sample Drop-Off Image