NGS Sample Submission

Sample Submission Guidelines
Sample requirements vary depending on application.  The following may be used as a guideline; however, always consult Core staff prior to sample extraction.
ApplicationQuantity*Min Concentration**Volume for QC***
Total RNA-Seq0.3 - 1 ug50 ng/ul3 ul
mRNA-Seq0.3 - 1 ug50 ng/ul3 ul
Nextera XT DNA1-2 ng0.2 ng/ul3 ul
Metagenomics12.5 -25 ng5 ng/ul3 ul
User Prepared Libraries≥5 nM15 ulN/A
*Please consult Core staff if your samples do not meet these minimum requirements.
**Based on validations by Core staff using a fluorometric assay.
***This is in addition to the volume required for processing.
  • Please schedule an appointment to discuss sample submission guidelines with Core staff prior to submitting samples.
  • Please fill in all information on the sample submission form.
  • Please do not submit your entire stock RNA/DNA sample to the Core.  When eluting or re-suspending, make two aliquots for submission.  This will prevent subjecting your sample to unnecessary freeze-thaw cycles. Make a 3 ul aliquot for QC and an additional aliquot for processing.
  • Samples will be put in the processing queue only after they have been received and pass all quality control metrics.
  • Use an established isolation method that produces an intact sample free of contaminants that may inhibit downstream applications.  It is best to elute in nuclease-free water when possible.  AVOID buffers containing EDTA and minimize carryover of salts, phenol, etc.
  • Submit samples in clearly labeled 1.5 ml tubes with the submission date and sample ID.
  • Prior to processing, samples will be quantitated using the appropriate Qubit fluormetric assay, and, if starting with RNA, sample integrity will be assessed on an Agilent TapeStation.
  • Biological replicates are always recommended to gain useful insight when performing data analysis.

Overall Sequencing Process

  1. Project Consultation: During project consultation, you will meet with the Genomics Core staff to discuss your research hypothesis and experimental design.  We will discuss sample requirements, replicate number, sequencing coverage, read length and output.
  2. Sample Submission: You must provide Genomics Core staff with a completed sample submission form at the time of sample submission.  
  3. Sample QC: Depending on the application, samples may be submitted to the Genomics Core as DNA, RNA, amplicons or library.  For best results, DNA and RNA should be of high quality and purity and should be intact (not degraded).  We recommend that DNA and RNA samples be resuspended in nuclease-free water to avoid the presence of inhibitors.  Prior to processing, we will run an Agilent TapeStation analysis to determine quality and a Qubit fluorometric assay to determine concentration.  
  4. Library Generation: The type of libraries generated will depend on the research question being asked.  The most frequently requested libraries are Illumina TruSeq Stranded mRNA, Illumina TruSeq Stranded Total RNA, ChIP, Nextera DNA and amplicon.  
  5. Library QC: Libraries are analyzed on an Agilent TapeStation to determine size and detect any contaminating products.  They are then quantitated using either qPCR or a Qubit fluorometric assay (this depends on the library type).
  6. Illumina Sequencing: Once the libraries pass QC and concentration is determined, they are ready for sequencing on either an Illumina MiSeq or an Illumina NextSeq 550.
  7. Data Delivery: When the run has completed, base calls are converted to fastq files in Illumina BaseSpace Cloud. You will receive an email containing run specifications and sample information, such as number of reads per sample. You will receive your data on a USB flash drive or external hard drive and will be given access to it through BaseSpace as well.
  8. Bioinformatics: Once your data is generated, the Genomics Core Facility is happy to assist you with analysis for certain applications, such as RNA-Seq and variant detection.  We will advise you regarding options for analysis during the initial project consultation.  You may also contact the LSUS Bioinformatics Core.

Samples will be put in the queue for processing ONLY after they have been received and pass all quality control measures.

Feist-Weiller Cancer Center Services

The Feist-Weiller Cancer Center Tissue & Serum Repository (TSR) provides service for automated RNA and DNA extraction on a Qiagen QIACube.  The current fees are listed below.

ServiceFWCC CostLSUH-S Cost
RNA Isolation
Tissue or Cell Pellet$7.50$10.00
Whole Blood$7.50$10.00
FFPE Section$9.00$15.00
FFPE Core Punch$10.00$17.00
Optional DNase Treatment$2.00$3.00
Genomic DNA Isolation
Tissue or Cell Pellet$5.00$7.00
Whole Blood$5.00$7.00
FFPE Section$7.50$10.00
FFPE Core Punch$9.00$15.00
  • All prices are per sample + $10 run fee (up to 12 samples per run).
  • An additional $20 prep fee will be added to each run of FFPE samples.
  • TSR will supply all reagents necessary for isolation including tubes for sample collections.
  • Samples will be returned to the user in 1.5 ml microcentrifuge tubes in a volume of 100 ul, unless otherwie requested.
  • Extraction from other sources available on a custom basis.

For more information please contact the TSR Technical Director:

Dr. Ellen Friday
(318) 675-4327