SERVICES AND FEES
Prior to project initiation, a meeting is required with CBC staff to discuss each project. If mutually agreed that the CBC can support the project, we will deliver a quote outlining the approach, timeline, and cost for the agreed service(s). As this is cutting-edge science, we cannot guarantee success, in all cases the user will be billed for cost and labor for CBC effort per our fee structure. After acceptance of the quote, the user will fill out and return the sample submission form provided with the quote, and also found on each CBC facility’s website. All samples are assumed to be safe, and no greater than BSL1, unless otherwise agreed upon in advance. The user must diligently and transparently followed all University of Illinois sample acquisition, movement, and safety protocols.
Our consulting rate (as of January 2020) is $70/hr. Our costs are based on estimates that encompass both this consulting rate as well as computational cost from processing and storing data. Projects also normally require some start up time for downloading data and updating databases and software.
Below are examples of genome/transcriptome sequencing analysis services that are offered through HPCBio. Individual quotes will be provided for specific projects, please email email@example.com for a current price estimate.
Genome Sequence Assembly
De novo genome assemblies. These include sequence data from:
- Illumina HiSeq and MiSeq (50x coverage or more) - ABySS, MEGAHIT, SOAPdenovo2
- 10x Genomics data (using Supernova)
- Long-read sequencing data from Pacific Biosciences and Oxford Nanopore (using Canu, FALCON, wtdbg2, Peregrine, or MaSuRCA
- Everything from bacteria and archaea to eukaryotic species (vertebrate, plant, algal, fungal)
On all assembly projects we highly recommend the following:
- Coordinate with our DNA Services facility to discuss the latest sequencing technologies and the best possible sample preparations for optimal assembly results
- For eukaryotic assemblies: perform an initial shotgun sequence analysis (20-25x coverage) for organisms where little information is known about ploidy or heterzygosity. We can utilize this in a standard k-mer-based analysis to determine how difficult the assembly may be.
- For bacterial genome assemblies: use long-read technology (PacBio or Oxford Nanopore), If using Oxford Nanopore or PacBio CLR data, also include a small Illumina MiSeq run to get the highest quality assembly. We have a workflow that can assemble these data and routinely can achieve fully closed, gapless assemblies (including plasmid sequences)
We can also perform followup quality assessment of assemblies against closely-related reference genomes for additional cost. Please contact us for more details if you are interested.
Transcriptome Sequence Assembly
De novo assemblies using next generation sequencing data from Illumina data. Assemblies can be evaluated using BUSCO and other tools along with input sample information to assess transcript abundance.
Annotation Of Genomes Or Transcriptomes
Includes ab initio gene prediction on draft genome assemblies followed by annotation based on sequence similarity to existing database sequences. We use the MAKER environment to customize annotations but can also assist in using alternative annotation pipelines, including Prokka, NCBI's Prokaryotic Genome Annotation Pipeline, or JGI's IMG pipeline.
Note the cost varies based on the number of annotation criteria used (e.g. InterProScan, multiple BLAST databases, multiple ab initio predictors, availability and quality of reference genome and transcriptome data, available ESTs, etc.)
Gene Expression Analysis
We have extensive experience performing differential gene/transcript expression analysis on a wide range of organisms and experimental designs, using data from RNA-Seq and numerous microarray platforms.
RNA-Seq analysis includes genome alignment, generation of gene and transcript counts, and quality assessment of data. Initial expression analysis includes read fate checks to assess how many reads mapped within annotated gene regions and generation of a list of differentially expressed genes.
Includes data preprocessing, statistical tests, and inclusion of easily available annotation information for any array type (cDNA, Oligo, and Affymetrix) using statistical program R (Bioconductor). Additional data mining, including gene clustering, GO and KEGG testing are available on a consultation basis.
Molecular Marker Discovery
Includes single nucleotide polymorphism, indels, simple sequence repeats discovery, extract molecular marker flanking sequences for designing genotype assays, and annotation of the markers. Since the complexity of individual projects can vary greatly, it is impossible to provide a typical cost.
Epigenomic Data Analysis
- ChIP-Seq - Identification of putative transcription factor binding regions, quality assessment, peak calling, retrieve neighboring gene context, annotation of binding regions, and differential binding analysis.
- Methylation - Bisulfite data analysis from both chip-based and sequencing-based data.
Targeted Microbiome Analysis
Fluidigm data analysis analysis using our custom analysis workflow
De novo assemblies of metagenome data, annotation of the assemblies, taxonomic/functional classification of raw read data, and other related analyses are also possible and are priced on a case by case basis.
We have experience with additional analyses not listed above, including ATAC-Seq, HIT-CLIP, MeDIP/MDB-Seq, Tn-Seq, shRNA, chromosomal replication, and custom pipeline development and optimization. If you have a more complex project, please contact us to discuss additional options for payment.
Also, let us know if you have specific needs on procedures and deliverables. These are being constantly revised and improved to keep pace with advances in bioinformatics, software, and computer infrastructure. We are open to customizing protocols and deliverables to your project.
Acknowledgement of work
All scientific work performed by the Roy J. Carver Biotechnology Center (CBC) is required to be acknowledged in scholarly publications, posters, and presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any CBC personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author.
***This is an abridged list of our service prices and subject to change at any time; please contact our Help Desk (firstname.lastname@example.org) for information on prices and other issues related to your project.***
Facility users not within the State of Illinois are subject to a 31.9% indirect cost rate. State of Illinois institutions are subject to a 31.9% indirect cost rate for Federally-funded projects, and 10% indirect cost rate for non-Federally funded projects. Off-campus projects require an off-campus user form, to be provided by the facility, and if over $10,000 a technical testing agreement. For further information contact Dr. Mark A. Mikel (217-244-0144; email@example.com ), Associate Director of the Roy J. Carver Biotechnology Center.
*All services are provided on a best effort basis and must be paid regardless of failure or success unless stated otherwise*