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Sample Input Guidelines

NGS technologies and GSAF procedures can accept a wide range of sample amount and quality. By following these guidelines, you greatly reduce the risk of failure or poor results from sample-related issues, but successful sequencing results are routinely obtained for lower quantity or quality samples.

NOTE: The concentrations listed below should be determined by fluorometry.  If you do not have access to a fluorometry-based assay (e.g. Picogreen/Qubit/etc.) and are relying on spectrophotometry, increase concentrations by at least ten-fold.

Please see notes below on guidelines for shipping tubes and plates

If you are submitting this...

For this platform...

GSAF requests...

Minimum recommended amount

Finished NGS sequencing libraries

Illumina HiSeq or MiSeq

20 ul @ >2 nM

0.01 picomoles per 1 million reads >50pM

DNA or RNA

BioAnalyzer QC only

10 ul > 1 ng/ul

4 ul > 50 pg/ul

DNA - genomic DNA, Must be high molecular weight or the read distributions will not be evenddRAD genotyping25 ul  @ 10 ng/ul25 ul @ 1 ng/ul
DNA - genomic DNA (NOTE: this assumes PURE POPULATIONS - i.e. 100% bacterial or fungal - you may need to assay samples with mixed populations prior to submission)Metagenomics (bacterial or fungal)25 ul @ 10 ng/ul FOR ALL SAMPLES SUBMITTED (i.e. customer must normalize input samples)25 ul @ 1 ng/ul

DNA - genomic DNA, high molecular weight, for library prep

Any platform, fragment library

5 ug @ > 20 ng/ul

1 ug @ > 10 ng/ul

DNA - genomic DNA, high molecular weight, for library prep

Any platform, mate-pair library 1.5-3kb

100 ug @ > 100 ng/ul

10 ug @ > 10 ng/ul

DNA - genomic DNA, high molecular weight, for library prep

Any platform, mate-pair library >3kb

500 ug @ > 200 ng/ul

200 ug @ > 100 ng/ul

DNA fragments (including IP-derived DNA) or DNA amplicons (PCR products), for library prep

Any platform

500 ng @ > 1 ng/ul

200 ng @ > 50 pg/ul

RNA* - total RNA, for library prep

Any platform

5 ug @ > 50 ng/ul, RIN>7

2 ug @ > 5 ng/ul

RNA* - mRNA, miRNA or other RNA sub-fractions, for library prep

Any platform

1 ug @ > 10 ng/ul

100 ng @ > 50 ng/ul

  • - NOTE: If you submit RNA, we recommend you prepare two 5ul aliquots for QC in addition to one primary aliquot for preparation while the RNA is thawed. This allows us to run QC on the aliquots without thawing and re-freezing the preparative aliquot.

Sample storage solutions

DNA or RNA can be provided in water, TE, low-TE, or other common storage solutions. If you are submitting your sample in something other than water or TE, please note this in either the Sample Description or Brief Job Description fields.

Marking your tubes and preparing to ship

Please write your sample names AND your job number ("JA1xxxx") on your tubes before dropping off or shipping to the GSAF lab at MBB 3.210. You will not receive your job number until your electronic submission has been approved by the lab. For any jobs with DNA that will have 12 or less samples please submit in 1.5 mL Eppendorf lo-bind tubes, but any 1.5 mL tube is acceptable.  Do not send 0.5 ml tubes.  For DNA jobs with greater than 12 the samples need to be submitted in a 96 well plate, when submitting your request please upload an excel file with a plate map into the supplemental data section.

If you are shipping your samples do not parafilm them if you have more than 8 tubes.  If you have multiple samples we suggest shipping them in some type of box for storage, either plastic or cardboard.  50 ml conical tubes are also acceptable, please do not place your samples loosely among of box full of dry ice for shipment, they should always be in a secondary container.

Submitting Samples in 96 well plates (Great for large jobs such as metagenomics and ddRAD, or any jobs for a large number of DNA samples)

Please be sure to write the job number on the side of the plate, if you are submitting multiple plates be sure to label them with a plate number, i.e. plate 1 JA1XXXX.  You will be required to submit a plate map that references wells to sample names, we ask that you include the actual well position in the sample name, i.e.  A1_Test123, B1_Test567 ect...The plate map can be uploaded using the supplemental upload function when submitting the job.

Please use skirted or semi-skirted plates, and seal with a foil.  Place a piece of cardboard or some protective barrier over the top of the foil for protection.  We would strongly recommend placing each plate inside its own box even if you are shipping multiple plates, be sure to throughly seal the plates!! 

Always place tubes or plates in a secondary container, never ship samples loose in a box of dry ice!

Shipping

Shipping information is available here

Sample purity

We encourage you to evaluate purity (e.g. OD260/280 or OD230/260/280) as a measure of your nucleic acid extraction process. We do not provide guidelines for these measures because most of our NGS procedures begin with steps that are highly tolerant of contaminants, followed by purifications. If your samples fail our in-process QC while internal controls do not, we will contact you to troubleshoot further.

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