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Genomic and RNA Profiling Core Facility

Houston, Texas

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Genomic and RNA Profiling Core
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SAQC for Concentration

Bring diluted samples on ice or dry ice for SAQC

  1. Users must submit a SAQC request on MAID and receive the confirmation email before bringing samples to the facility.
  2. Users must submit RNA samples diluted to 25ng/µl - 500 ng/µl for Nano Chip Analysis or 200pg/µl - 5,000 pg/µl for Pico Chip Analysis. We will test the samples for integrity and concentration using the Agilent 2100 Bioanalyzer and the NanoDrop® ND-1000 Spectrophotometer. Please note: the sample must be delivered by a lab member who is registered on MAID (see user guide).
  3. For all other genomic DNA SAQC: Users must submit 50-100ng/uL in 5uL. Note that for ChIP-on-chip DNA, users will have to perform the QC steps themselves. The GARP will quantitate gDNA samples on the Qubit, Nanodrop, as well as on a 2% agarose gel.
  4. For Affymetrix SNP Chips only: Users must submit genomic DNA samples diluted in TE Buffer from TEKnova (product # T0223) to 100ng/ul in 5ul. We will test the samples for integrity and concentration using the NanoDrop® ND-1000 Spectrophotometer and a 2% agarose gel. Please note: the sample must be delivered by a lab member who is registered on MAID (see user guide). For the complete SNPs protocol, please visit the Affymetrix website.
  5. Note for Next-Generation DNA submissions consisting of ChIP, PCR product, or user prepared libraries: the GARP will run test these samples on the Nanodrop, the Qubit, as well as the Bioanalyzer. ChIP LIBRARIES: Samples will be returned to users prior to GARP cluster generation so the user can confirm at least 2x enrichment is intact.
  6. GARP technicians will test the RNA/DNA samples and provide users with concentrations and a quality judgment (i.e., "Pass" or "Fail" sample). These results can be observed in MAID after downloading the Agilent 2100 Expert software.
    Agilent Expert Review Software for Molecular Assays (DNA/RNA)
  7. For ChIP-on-chip users: Please be aware that the GARP must see your QPCR data from your samples and positive control from both the post-ChIP processing as well as post-amplification. We cannot pass your SAQC Request without the data. If you did not run a positive control, you (or your PI if you are not the PI) will need to sign-off on your samples. The sign-off releases the GARP from any responsibility of inadequate sample or chip performance. For more information on ChIP-on-chip QC measures, please visit Affymetrix Tiling Arrays.

  8. When the experiment is completed, users will be notified by automatic email that the results are available via MAID. No hard copy will be provided unless it is specifically requested.

Note: Samples will be automatically discarded two weeks after completion.

Please note: The GARP does not normally dilute users' samples. It is the users' responsibility to dilute the samples submitted to the proper concentration (25-500 ng/µL) for the Nano Chip Analysis or (200-5,000 pg/µL) for the Pico Chip Analysis. The GARP will charge a dilution fee of $25.00 for all RNA samples submitted for quality check that are not at the proper concentration range.

Please bring all samples in a 1.5 ml tube. We will not accept 0.6 ml or 0.2 ml tubes.

In order to open a SAQC result file emailed to you by GARP, you will need to download and install the data review software freely available from the Agilent web site.

Note: Users interested in picking up samples from the GARP should plan to pick them up at the following times: Monday and Friday 1-3 p.m.

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