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

Sequencing and Library Prep Services

Service type
Sample type
Amount
Volume
Platform
Sequencing only
NGS Final libraries for sequencing
>2nM
≥20ul
Illumina NovaSeq, NextSeq, MiSeq
 Standard DNA library prep 
high MW genomic DNA/ fragmented DNA/Amplicon/ IP derived DNA
1-80ng/ul
≥25ul
NovaSeq, NextSeq, MiSeq
Covaris fragmentation +BA
genomic DNA
1-80ng/ul
≥25ul
Covaris
Metagenomics (bacterial or fungal) 
DNA - genomic DNA (NOTE: this assumes PURE POPULATIONS
10ng/ul FOR ALL SAMPLES SUBMITTED (normalize input samples)
≥25ul
Illumina NovaSeq, NextSeq, MiSeq
RNA seq + Poly A enrichment
total eukaryotic RNA
10-80ng/ul
≥25ul
Illumina NovaSeq, NextSeq
RNA seq +Ribosomal depletion
Total RNA-Human, Mouse Rat
2-250 ng/ul
≥25ul
Illumina NovaSeq, NextSeq
RNA seq +Ribosomal depletion
Total RNA -Plant
2-250 ng/ul
 
Illumina NovaSeq, NextSeq
RNA seq +Ribosomal depletion
total RNA-bacteria
2-250 ng/ul
≥25ul
Illumina NovaSeq, NextSeq
RNA-Seq, no removal or enrichment
total RNA
1-200ng/ul
≥25ul
Illumina NovaSeq, NextSeq
RNA-Seq, no removal or enrichment
mRNA
.2-20ng/ul
≥25ul
Illumina NovaSeq, NextSeq
Small RNA library prep
 total RNA- for miRNA or other RNA sub-fractions
20-200ng/ul
≥25ul
Illumina NovaSeq, NextSeq
 Small RNA library prep
purified small RNA
2-20ng/ul 
≥25ul
Illumina NovaSeq, NextSeq
TagSeq
total eukaryotic RNA
10-100 ng/ul 
≥25ul
Illumina NovaSeq, NextSeq
Service
Platform
Sample Type
Concentration
Volume
Assay Type
QC only
Bioanalyzer only
DNA
>50pg/ul
4-5 ul
Bioanalyzer-DNA
QC only
Bioanalyzer only
total RNA
25-500ng/ul
4-5 ul
Bioanalyzer-RNA 6000 Nano
QC only
Bioanalyzer only
mRNA
25-250ng/ul
4-5 ul
Bioanalyzer-RNA 6000 Nano
QC only
Bioanalyzer only
total RNA
.05-5ng/ul 
4-5 ul
Bioanalyzer-RNA 6000 Pico
QC only
Bioanalyzer only
mRNA
.25-5ng/ul 
4-5 ul
Bioanalyzer-RNA 6000 Pico
QC only
Bioanalyzer only
small RNA-total RNA
1-100ng/ul
4-5 ul
Bioanalyzer- RNA 6000 Nano/Pico
QC only
Bioanalyzer only
enriched small RNA
1-20ng/ul
4-5 ul
Bioanalyzer-small RNA
QC only
Qubit-only 
DNA and RNA
variable
3-4 ul
qubit-only 
QC only
Plate reader service
DNA only
variable
6 ul
Plate reader service

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 ("JA20xxx") 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/RNA for library prep 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/RNA jobs that need library prep 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 (Required for large jobs)

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 JA20xxx.  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 if shipping the samples.  We would strongly recommend placing each plate inside its own box even if you are shipping multiple plates, be sure to thoroughly seal the plates!!

Samples should be plated starting at A1 then plate the samples vertically, A1 to H1, then A2 to H2 and so on.....Do not skip wells, you will be charged for wells that are skipped and we will not process samples that are plated A1 to A12.

The GSAF does not guarantee read counts but we will try our best to meet customer request when we prepare the libraries, however we will not make up any read counts for customer prepared libraries.

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.