Whole-genome sequencing
Shotgun DNA Prep
Watchmaker Genomic's robust and flexible whole-genome library prep. Our option for large genomes and DNA of any quality (including FFPE samples). PCR-free and fragmentation-free workflows are available. Can accommodate inputs of 1-250 ng of DNA per sample suspended in water or low-EDTA buffer.
Mini Echo DNA Prep
A miniaturized, very low-cost Nextera library prep designed for genome skimming projects. Suitable for small to medium genomes and DNA of moderate quality or better (>50% of DNA fragments over 1000bp). Requires >25ng of DNA per sample suspended in 25-50ul of water or buffer that is free of EDTA.
RNA
Stranded RNA-seq
Stranded, high-complexity RNA-seq libraries for RNA of any quality. Available with or without bead-based mRNA capture. Requires >5ng of total or enriched RNA suspended in 25-50ul of RNase-free water.
Small RNA-seq
RNA sequencing for miRNA and other small non-coding RNAs. Requires >5ng of total or enriched RNA suspended in 25ul of RNase-free water.
Single-cell
10X Chromium X
We offer a large variety of single-cell preps on Chromium X. All sample-agnostic 10X preps require viable cells or nuclei and can prep up to 20k cells per sample; these include gene expression, ATAC-seq, and multiomic single-cell library preps. Samples for sample-agnostic 10X preps must be submitted as viable single-cell or nuclei suspensions; contact us to schedule a sample hand-off time.
For human, mouse, and rat samples we have the option of using Flex Apex gene expression. Apex allows for fixation of samples and uses plate-based combinatorial barcoding upstream of microfluidics to prep up to 1M cells or nuclei from up to 384 samples. Multiplexing greatly reduces the per-sample cost of library prep and fixation allows for flexibility in sample collection. Samples for Apex must be submitted as fixed and quenched single-cell or nuclei suspensions.
BioRAD ddSEQ
ddSEQ offers a lower per-sample cost for projects requiring a smaller number of cells. ddSEQ single-cell gene expression and ATAC-seq assays can accept up to 7k viable cells or nuclei per sample and are sample-agnostic. Cells or nuclei suspensions must have a high viability for successful prep; contact us to schedule a sample hand-off time.
Parse Evercode
Parse preps use combinatorial barcoding to identify individual cells within each sample. These gene expression preps are priced by the total number of cells to be prepared, as the total cells in each kit can be divided across multiple samples. Available kit sizes are Mini (10k cells, up to 12 samples), WT (100k cells, 48 samples), Mega (1M cells, 384 samples), and Penta (5M cells, 384 samples). Cells or nuclei must be submitted as fixed single-cell or nuclei suspensions.
Hi-C
Phase Genomics’ proximity ligation protocol, typically used alongside long-read data to reach chromosomal-level assemblies. Requires >50mg of flash-frozen tissue. Other preservation methods, such as RNAlater or ethanol, are acceptable but may impact library yield or complexity.
16S
Amplification of the 16S region by PCR. We offer barcoded primers, allowing up to 768 samples to be pooled for sequencing.
If you don’t see the right prep or aren’t sure what you need, email us at genomics@uoregon.edu.