The UNL Bioinformatics Core Research Facility (BCRF) is located on the City Campus of the University of Nebraska-Lincoln, and is part of the Center for Biotechnology which houses several other cores. We offer rich standard and custom bioinformatics services for a reasonable price and timely turnaround, and can provide outstanding service from data quality assurance all the way to publication-ready graphs and data deposition to standard repositories.
Our average turnaround time is approximately 7 business days for most services, thanks to our HPC Linux compute cluster and priority-access to the University's supercomputing cluster for larger analyses.
Most recent publication:
Sinha R, Clarke J, Riethoven J. Metabolic Syndrome, Gut Microbiome and Dietary Bioactive Peptides, an Unexplored Triad. Diabesity, v. 4, n. 1, p. 1-4, jan. 2018. ISSN 2369-0569. doi:http://dx.doi.org/10.15562/diabesity.2018.45.
Although we are new on the Science Exchange platform, we have a long track record of providing high-quality and timely bioinformatics analysis services to academia, predominantly, and to biotech SMEs. We understand that even today the massive amount of data generated by NGS-based studies can come as a shock, but we are here to help you manage the data, analyze it, and gain insights from the results.
Some of our most requested services are (please check under the individual services for more details):
Any of these can be combined or integrated with other or customized services, just ask us for a quote. All services that are based on sequencing come with complimentary quality control and assurance of your raw data (adapter removal, filtering/trimming) - we will only continue with any analysis if your data passes muster for the requested service.
We do a lot more then we could list here - please contact us for further information on how we can enable and speed up your research.
Turnaround time for projects are 1-2 weeks on average.
Custom analysis and/or coding starts at $70/h - mostly this is for items that cannot be captured in one of our main services. We can give you a firm quote on any custom needs after discussion(s).
The BCRF has both its own Linux cluster (250 cores, 140TB storage) and priority access to the University of Nebraska Holland Computing Center (~15,000 cores, ~3PB storage), enabling to finish compute of even massive analyses in short order.
We keep all data, from raw data to final results, for 90 calendar days. You can opt for us to remove it earlier (no cost, but irrevocable), or to keep a two-location backup of your data until publication (at $50/TB one-time fee).
Note: if you are faculty or staff at an academic or government institution and need bioinformatics support or collaboration for a long(er) term, it would be more advantageous to write us into grant proposals, as then we are more flexible to help you beyond the scope of individual orders.
We provide gene expression profiling on a per-sample basis, i.e. each control, treatment, condition, tissue, etc. is deemed a sample. Within each sample you should have several biological replicates (more is better, no additional cost).
This service has as deliverables:1) QA of raw data, with adapter removal and quality trimming. Before- and after QC graphs and statistics table. Filtered sequences that are used in subsequent steps are also by standard provided back to you. 2) Alignment of the sequence against a reference species; we normally use the newest build and source but there is an option to use any build or version. Mapping statistics for each replicate and a summary for each sample are provides, as are BAM and BigWig files (to display alignments and expression on a Genome Browser). 3) Files with gene- and transcript-level expression quantitation. 4) Tab-delimited files for each combination of samples, listing test-statistics and fold changes for each gene AND additionally files where we only list the significantly differentially expressed genes and transcripts. Comes with gene symbol, functional description, and Gene Ontology identifiers (where known) standard. 5) Hierarchical clustering of all individual replicates, clustering of only up/down regulated significant genes. 6) A full report that lists all methods, software and database version, references, and all graphs as 600dpi.
Note 1: if a species is sparsely annotated, we do a best-effort annotation by inferring function with our in-house pipeline at a one-time cost of $200 per project.
Note 2: we can do this analysis for species with no reference genome as well - this will incur a fee for transcriptome assembly, gene prediction, and annotation. We'll quote that on a case-by-case basis depending on the taxonomic Kingdom and the presence of closely related taxonomic units.
Note 3: by default we keep all the data and results for 90 calendar days. If you require longer access (up to publication), please let us know.
Please see our 'Bioinformatics' service for more upfront information and our different pricing options depending on the individual services you require. Ask for a quote for specific information.
Our average turnaround time is between one and two weeks.
Sequencing Data Analysis Services
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