If the right prep for your project is not listed below or you aren’t sure what you need, reach out to us at genomics@uoregon.edu to discuss.
Illumina Library Prep
Whole-genome Sequencing
Mini Echo DNA Prep
A very low-cost Nextera library prep miniaturized using our Echo liquid handler. Suitable for small to medium genomes and DNA of moderate quality or better.
Shotgun Prep
Whole-genome sequencing using enzymatic fragmentation. Our option for large genomes and DNA of any quality. A PCR-free workflow is available.
RNA
Stranded RNA-seq
Stranded, high-complexity RNA-seq libraries for RNA of any quality. Available with or without bead-based mRNA capture.
Small RNA-seq
RNA sequencing for miRNA and other small non-coding RNAs.
16S
Amplification of the 16S region by PCR. We offer barcoded primers, allowing up to 768 samples to be pooled for sequencing.
Hi-C
Phase Genomics’ proximity ligation protocol, typically used alongside long-read data to reach chromosomal-level assemblies.
Single-cell
3' Gene Expression
3' gene expression at the single-cell level. We offer GEX from 10X, Parse, or ddSeq. Reach out to discuss which platform best fits your project.
ATAC-seq
Chromosomal accessibility information at the single-cell level. We offer ATAC-seq from 10X and ddSeq.
Multiome
Combined 3' GEX and ATAC seq data at the single-cell level. 10X is the only platform for this protocol at this time.
PacBio Library Prep
Amplicon Sequencing
Amplicons 500-10,000bp can be prepped for sequencing on Revio using a standard SMRTbell library prep. We offer 96 SMRTbell barcodes for multiplexing, but recommend that you incorporate barcodes during PCR to reduce overall prep cost.
Kinnex
Kinnex library prep concatenates together individual inserts to increase the number of reads yielded from one SMRTcell.
Full-length 16S
12-mer concatenation of full-length 16S amplicons. We have 96 full-length 16S barcodes and 4 Kinnex SMRTbell barcodes available, allowing up to 384 samples to run on one SMRTcell.
Full-length 10X cDNA
16-mer concatenation of 10X cDNA product.
Full-length RNA
8-mer concatenation of IsoSeq full-length RNA. We have 12 IsoSeq barcodes and 4 Kinnex SMRTbell barcodes available, allowing up to 48 samples to run on one SMRTcell.
RNA Submission Requirements
- Strongly recommended to use samples with RIN/RQN >7.
- Samples have been treated with DNase and there is no remaining DNA present.
- A minimum of 50 ng/µL total RNA in at least 10 µL of nuclease-free water.
- If you plan to prepare your own cDNA, please contact us to coordinate downstream compatibility. Submit 200-600ng of purified, multiplexed cDNA in EB.
Whole-Genome Sequencing
PCR-free library prep of native DNA, generating 10-30kb HiFi reads with 5mC calls. Up to 96 WGS libraries can be pooled for sequencing.
WGS Submission Requirements
PacBio library prep and sequencing success is highly dependent on the quality of input DNA for library prep. Please adhere to the following guidelines when submitting DNA samples for library prep.
- >50% of the gDNA must be >30kb in length
- Nanodrop 260/280 ratio = >1.8
- Nanodrop 260/230 ratio = 2.0 - 2.2
- No visible particulates, dust/lint, precipitates, colors, or cloudiness
- A total of 2 µg of dsDNA per SMRTcell is required (5 µg is preferred).
Extraction
DNA
High-throughput
Extraction of plant or animal tissue on our Kingfisher. Requires submission of 8+ samples in matrix tubes, which we ship to you at the start of your project.
Standard
Manual extraction of DNA for smaller projects.
High Molecular Weight
Extraction of high molecular weight DNA for long-read applications. We use a variety of different protocols depending on the tissue type, including NanoBind Pan DNA from PacBio and Qiagen Genomic tips.
HMW Tissue Submission Requirements
Freshly-harvested tissues should be flash-frozen in liquid nitrogen and stored at -80°C. Other preservation methods, such as RNAlater, typically result in poor sequencing performance.
Amount of tissue required:
- For plant extractions, provide at least 3-5g of flash-frozen young leaves
- For animal extractions, provide one of the following:
- >1g of low-DNA-content tissue (muscle, skin)
- >100mg of high-DNA-content tissue (liver, spleen)
- >50 ul of blood containing nucleated RBC
- >500 ul of blood containing non-nucleated RBC
- For cultured bacteria, >20M cells
For other extractions, mass required will vary substantially depending on your organism, tissue, and sequencing application. Please email genomics@uoregon.edu to discuss.
RNA
Extraction of RNA using Zymo Direct-Zol. We recommend flash-freezing or storing in a stabilizer such as Trizol or RNAlater.
Quality Control
Fragment Analysis
Automated capillary electrophoresis for measuring fragment sizes in a sample. Fragment analysis is included for all samples submitted for sequencing; if you are submitting a single tube for sequencing, you do not need to request fragment analysis separately.
We offer the following Fragment analysis types, and require 3 ul of sample within the appropriate concentration range for submission:
- NGS (DNA 1-6000 bp), 0.1-10 ng/ul
- Large Fragments (DNA 75-165,000 bp), 0.5-2 ng/ul
- RNA High Sensitivity, 0.1-10 ng/ul
- RNA Standard Sensitivity, 5-500 ng/ul
Purification
Standard Bead Cleanup
Magnetic bead-based purification of samples in 1.5 ml tubes or 96-well plates. If you would prefer to run your own bead purification, we also offer Omega beads for purchase by UO researchers through iLab.
DNase or RNase Treatment
Enzymatic removal of contaminating DNA or RNA from user-submitted sample.
Size Selection
Sage BluePippin
Automated size selection of nucleic acid fragments anywhere between 50 and 50,000 bp in size.
Bead-based Size Selection
Remove small fragments (up to 3 kb) from DNA extractions or completed libraries. If you would prefer to run your own bead size-selection, we also offer Omega beads for purchase by UO researchers through iLab.
Multiplexing of Illumina libraries
qPCR quantification followed by equimolar pooling for sequencing. Only required when submitting more than one tube for multiplexing on an Illumina lane.
Normalization
High-throughput normalization of user-submitted extractions to a desired concentration on our Hamilton Vantage robot.
Speedvac Concentration
Concentrate up to 4 plates of samples on our Centrifugal evaporator. The Speedvac is also available for reservation through our instrument reservation system.