Guidelines for Submitting NGS Samples

Investigators can submit samples in isolated genomic DNA, Total RNA, ChIP-DNA, fragmented DNAs, or other samples, including BACs, amplicons, MBDCap-DNAs RIP-RNAs for sample preparation and sequencing, or NGS libraries for sequencing. Submitted samples will be analyzed by appropriate quality control measures (Qubit, Bioanalyzer, or gel electrophoresis) to assess the quantity and quality of the sample. You will be notified if there are any issues regarding the quality and quantity of the sample. Samples that pass quality control steps are then put through a series of steps to create a sequencing library using the appropriate sample prep kit.

In order for us to provide you with high-quality data, please review the following information for details on how to submit samples to GCCRI Genome Sequencing Facility.

The sample submission form must accompany all submitted samples (Sample Submission Form). It is essential that you fill out all the information. Please note: Sample_Name field entry in the sample submission form cannot contain illegal characters not allowed by file systems. Allowed characters are alphanumeric characters and underscores. Examples of common characters not allowed are the space character and the following:? ( ) [ ] / \ = + < > : ; ”

Please label each sample individually and carefully to make sure we can recognize all your samples. Please include a sample submission form in your sample package. DNA form samples should be on ice or dry ice, and RNA form samples should be on dry ice packages.  Samples submitted to the GSF should be sent in 1.5 mL tubes, PCR strip tubes, or 96 well plates, and labeled & sealed well. Please do not place your samples loosely among of box full of ice or dry ice package, they should always be in a secondary container such as a box, bag, or tube.

Generally, samples can be submitted in three different forms: DNA, Total RNA, and PCR amplicon product. For sequencing application and the starting material, see the table below.

Sequencing Application Sample Type Quantity* Vol. (ul) Suggested Conc.(ng/ul) Sample Quality
DNA-Seq (genome< 5Mb) gDNA 10-50 ng >10 1-10 Pure and intact
DNA-Seq (genome> 5Mb) gDNA 10-1000 ng >10 10-100 Pure and intact
mRNA-Seq Total RNA 100-2000 ng >10 25-200 RIN >7
Total RNA-seq Total RNA 100-2000 ng >10 25-500 RIN >4
SmRNA-Seq Total RNA 100-1000 ng >10 25-100 RIN >7
ChIP-Seq ChIP- DNA 0.1-50 ng >10 0.1-10 Bioanalyzer trace file or gel pic
Exome Enrichment gDNA 50-1000ng >10 5-200 Pure and intact

 

If submission library:

Sequencing Libraries Volume (ul) Suggested Qubit Conc. (ng/ul) Measurement (Qubit, Q_PCR) Requirement
Individual library 10 1-10ng/ul If no QC is needed, need to provide Bioanalyzer trace file
Pooled library 20 1-10ng/ul Need to have at least 5nM pool concentration

*We strongly recommend using fluorometric-based methods for accurate quantification, such as Qubit or PicoGreen assays, to measure the concentration. If you don’t have access to the equipment mentioned above and have only a nanodrop reading, we suggest you plan to give us double or triple the amount of starting materials.  In general, concentrations measured by nanodrop are higher than the actual concentration. Please mark the equipment you used for quantification.

These amounts are guidelines only. For specifics, please contact Zhao Lai, Ph.D. Director of Genome Sequencing Facility.

Zhao Lai, Ph.D.
email: laiz@uthscsa.edu
phone: 210-562-9246
fax: 210-562-9135

 

Users on campus can drop off the samples (DNA form samples should be on ice or dry ice and RNA form samples should be on dry ice).

GCCRI building address:
Genome Sequencing Facility
Room 2.120
Greehey Children’s Cancer Research Institute
8403 Floyd Curl Drive, San Antonio, Texas 78229
Attn: Mandy Hinojosa
Phone 210 562-2222
Attn: Korri Weldon
Phone 210 562-9125