Below is a list of some of the services available to microbiome researchers at UCI, provided by the Genomics High-Throughput Facility in collaboration with the Microbiome Initiative.
Consultation: Advice on Project Planning.
Training: Hands-on workshops for microbiome sample collection, sequencing preparation, and data analysis.
DNA or RNA extractions: DNA/RNA extractions from your samples.
High molecular weight DNA preparation: DNA extraction for PacBio sequencing. Long-read sequencing of microbial isolates provides high quality assemblies of whole genomes.
Amplicon library preparation: PCR amplification of a conserved gene region to characterize the taxonomic composition of bacteria (16S) or fungi (ITS) with the ability to multiplex many samples on a single sequencing run.
Metagenomic and metatranscriptomic library preparation: Library preparation for DNA/RNA sequencing of isolates or communities.
Quality checking of libraries or individual samples: Methods vary depending on the samples. Types of assays include:
- Bead Cleanup
- Nanodrop
- Qubit
- Qubit & library pooling
- Kapa qPCR
- Bioanalyzer HS DNA
- BluePippin size selection
Sequencing of whole genomes, amplicon libraries, metagenomes and metatranscriptomes: Illumina MiSeq, HiSeq 4000 and NovaSeq for short reads; PacBio Sequel II for long reads.
Bioinformatics: Amplicon libraries data can be provided as raw data and/or as an OTU table after initial qiime2 analysis.
Statistical analysis: General statistical advice provided at free consultation hours. More advanced statistical analyses and publication quality graphics available as a fee-for-service.