Guidelines for Submitting Samples
Nucleic Acid Submissions
You must submit QC information with your samples including: qubit concentrations and/or Bioanalyzer traces. If you do not have access to this equipment please let us know.
DNA Sample Submission
Please submit a labeled 1.5 mL tube microcentrifuge tubes along with your name, sample names, date, submission sheet and QC information (Qubit quantification and gel image) performed on the samples. The Genomics Core recommends that genomic DNA (gDNA) submitted for sequence analysis be purified using the QIAamp DNA kit or comparable gDNA isolation kits. RNase treatment of gDNA is required. Submit gDNA samples in nuclease-free H2O or reduced EDTA TE buffer (10mM Tris, 0.1mM EDTA pH 8.0). DNA samples must be QC'ed using qubit and submitted with the proper concentration or they will take longer to process.
- gDNA-Seq - a total concentration of 1 ug in a minimum volume of 20 ul
- ChIP-Seq - 25 ng Single ChIP enriched DNA in 30ul nuclease-free H2O
RNA Sample Submission
Please submit Total RNA in elution buffer or nuclease-free H2O with a final volume of 1 ug in a labeled 1.5 mL microcentrifuge tubes along with your name, sample names, date, submission sheet and QC information (Qubit quantification and Bioanalyzer report) performed on the samples. The RTSF Genomics Core recommends that total RNA be purified using the a TRIzol® based reaction or, if retention of miRNA is not required, most commercial isolation kit are acceptable. DNase treatment of RNA samples is required. Samples must be QC'ed with a qubit concentration and a Bioanalyzer trace or they will take longer to process. Submit RNA samples in nuclease-free H2O at the following concentrations:
- mRNA-Seq: 100 ng/ul, 1-4 ug Total RNA, > 10ul < 50ul volume.
- small RNA-Seq: 250 - 500 ng/ul, 2-3ug Total RNA.
Note: Extra volume is appreciated in the event of an error or library re-prep
Investigator Prepared Library Submission
- If multiplexing samples please include the list of the index tags used.
- We make every effort to accurately determine library concentration and sequencing dilutions using a combination of qubit, Bioanalyzer trace and Kapa qPCR. It is our recommendation that all libraries, produced in house or in other labs, have this information associated with them in order to predict the most accurate loading concentration. The Genomics Core will document the quantitation process for all libraries submitted in order to make the best decision given the information available to produce a successful run. If it is discovered that the library in question has an issue the customer will be notified and the final decision on whether it will be sequenced lies with them. If a library is run against Core advice, the Genomics Core is not responsible for the failed sequencing run as we cannot guarantee performance or output for libraries generated outside of our facility. If proper QC information is not available all submitted libraries are subjected to a charge for QC to ensure the highest quality data generation.
- All user prepared libraries are run on a per lane basis. The Genomics Core will not combine your samples with other submittor's samples. Various sized libraries do not perform uniformly on the sequencer and mixing can have negative effects. The Genomics Core recommends only pooling libraries of similar size.
- Please provide 15 ul of prepared library at a concentration of 10 nM for the HiSeq 4000 and NextSeq 500 and 4 nM for the MiSeq in 1.5 ml microcentrifuge tubes. If the volume of the library is less than 15 ul the there is a chance that it cannot be accurately quantified, 3 ul will be used for QC. If the library cannot be quantified due to low volume we cannot guarantee that the sequencing run will be successful.
Please submit all NGS samples in our LIMs before sending to the RTSF Genomics Core. Samples can be hand delivered to the RTSF Genomics Core and left in the refrigerator located in the hallway outside 24 hours a day. If you are mailing samples please ship them per the instructions above and send them to the following address:
c/o Shari Tjugum-Holland
612 Wilson Road, S-18B
East Lansing, MI 48824
*Please notify us of shipment and we can confirm receipt.