WELCOME TO USU BIOINFORMATICS CORE FACILITY
Ideas and breakthroughs fueled by computational prediction and next generation sequencing.
Our group has been contributing to different research projects by providing support and expertise in programming and advanced data analysis, focusing primarily on high-throughput genomics technologies. These include microarrays, genotyping, and next-generation sequencing (RNA-seq, ChIP-seq, SNP-seq, etc.). We also provide virtual server environments, secure public web portals, a large suite of open source applications, and hands-on tutorials and workshops on a wide variety of informatics topics, as well as custom data analysis and consultation services. We commit to the establishment of research collaborations with scientists from different departments.
We can perform a variety of analysis pipelines to mine your next-generation sequencing data.
RNA-seq
Whole transcriptome shotgun sequencing (WTSS) uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. RNA-Seq is used to analyze a changing cellular transcriptome.
ChIP-seq
In order to analyze protein interactions with DNA, ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
Methyl-seq
Bisulfite sequencing is the use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the most studied.
SNP genotyping
SNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms (SNPs) between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation.
miRNA-seq
MiRNA-seq is the use of next-generation sequencing or massively parallel, high-throughput DNA sequencing to sequence microRNAs. miRNA-seq differs from other forms of RNA-seq in that the input material is enriched for small RNAs.
These are answers to commonly asked questions. More information can be found here.
What kinds of services does BioinfoCore USU provide?
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How do we check the quality and trim/filter low quality reads?
One can run FastQC and FASTX tool kit
What length of reads are required for RNA-seq?
Anywhere between 50 and 75 base pairs is sufficient for simple RNA-Seq analysis
How many replicates are needed for RNA-seq?
While collecting replicate data can be expensive, you'll need at least 3 replicates for an accurate analysis
Resources for RNA-Seq analysis:
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A leading provider of Bioinformatics data analysis and consulting.
