Services
Let's make a plan
Gathering pilot data? Planning a study for a grant or a manuscript? Fill out the project inquiry form and email it to us here
Pre-award Consulting
We are available to help investigators planning for grants involving epigenetics research. As part of our pre-award consulting and support we will provide:
- Revision of the study design
- Letter of support
- Budget
- Partial FTE from computational biologist available
- Description of experimental and computational methods
In order to receive the best support please reach out at least 3 weeks before the grant deadline by emailing us here
Study Design and Sample Preparation
In order to maximize chance of success and rigor, each study needs to be carefully designed. For this reason, we ask investigators to meet with us at the very beginning of their study so that we can discuss:
- Experimental assay selection. We help selecting the appropriate assay(s) based on the investigator’s questions and budget.
- Number of samples and experimental groups. The size of your study will depend on different factors, but we generally discourage groups smaller than n=4 when possible.
- Sequencing strategy. This includes estimating the adequate coverage, read length, and instrument. We work in close collaboration with the MPSSR and the GC3F for sequencing.
- Sample preparation and submission. High quality samples are key for successful experiments. Please, see our requirements for sample submission.
We offer bioinformatics analysis of next-generation sequencing data so that projects can be done end-to-end and we can be a one-stop shop for investigators. After submitting the next-generation sequencing libraries to the sequencing core, we monitor as they move through their pipeline. When ready, we download the sequences (fastq files) and copy them to our server.
Assays offered:
- RRBS
- WGBS
- Low-input WGBS
- ATACseq
- RNAseq
- scRNAseq
- HiC
Data QC & Standard Analyses
Our standard analysis includes quality assessment of the sequencing data received from the investigator of the sequencing core and generation of summary statistics (i.e. raw and filtered read counts, alignment rates). Moreover we will perform data exploration techniques such as principal component analysis and clustering. Finally, we will perform differential analysis across groups as indicated by the investigator's study design. Besides the result files, we will provide a detailed report describing each step of the data QC and analysis.
Software we commonly use includes:
- MultiQC
- DESeq2
- Limma
- methylKit
- ChromHMM
Custom Analyses
Some projects are more complex than others and require the development of unique bioinformatics pipelines. If you have a project that deviates from the standard analysis, we will work with you to determine an efficient and cost-effective approach.
FAQ
- What is a typical turn around time for bioinformatics analysis?
- The turn around time for the bioinformatics analysis varies greatly depending on the nature of your data, the study design, analysis requested, and also on the overall work load of the service core at the time. A typical project often takes ~3 weeks to finish from the time our bioinformatics team starts the analysis.
- What data is provided to clients following bioinformatics analysis, and how?
- The exact results provided depends to the analysis requested. Once the analyses are completed we upload the raw data, along with the results and analysis reports on the secure OHSU-based cloud service called Box. We send you the link to this data and you can easily access your data for downloading.
- What skills/software are required to handle the results?
- Proficiency in Microsoft Excel is crucial for exploring the results summary tables. Familiarity with the UCSC genome browser and the igv data visualization tool is extremely helpful in exploring the epigenetic and genetic landscape of regions of interest. Tutorials for these browsers are available online. Moreover, EC personnel can provide some personalized training.
- What kind of sequencing should I do?
- Our assays are based on Illumina sequencing. the specific platform, read length, and coverage will depend on the assay and will be selected by the EC.
- How can I determine if my project requires a standard or custom analysis?
- Most projects can be done using our established computational pipelines. However, some projects might require for us to create custom pipelines to address additional questions. The EC will be in constant communication with the investigator in order to find the most cost-efficient but rigorous approach.
Chromatin Analysis
Chromatin is made of a combination of proteins (histones) and DNA. Chromatin structure is shaped by histone modifications and transcription factors and influences gene expression. Moreover, chromatin remodeling occurs during development and as the result of treatments. The assays below are used to study chromatin structure.
Hi-C sequencing is a type of chromosome conformation capture that allows an examination of chromatin organization in the cell. This technique allows investigation of long-range genomic interactions, such as the ones between promotors and enhancers. Hi-C data processing yields genomic compartments and topologically associated domains (TADs), informing which genes might be co-regulated.
For Hi-C applications, see here: https://arimagenomics.com/publications
DNA Methylation Analysis
DNA methylation is a chemical modification of the DNA by which methyl groups are added to the DNA molecule. In mammals, methylation is added to CpG sites. DNA methylation changes the activity of genes or regulatory elements, without changing the sequence. We offer different types of DNA methylation profiling, all based on next-generation sequencing. A description of these methods and how they compare with each other is provided below
Services
Whole-genome bisulfite sequencing (WGBS) allows for base-pair resolution quantification of DNA methylation across the whole genome. Although this method is considered the gold standard, it is also the most expensive as high-coverage sequencing is required across the whole genome. Advantages of WGBS include that it can be applied to all species and has low DNA input requirements ( >10 nanograms).
Reduce Representation Bisulfite Sequencing (RRBS) uses digestion with the restriction enzyme MspI to analyze a portion of the genome where DNA methylation occurs (i.e. promoters, CpG island, CpG shores). This approach still generates a genome-wide map of DNA methylation but the sequencing costs are substantially lower than WGBS. This approach can be used in all species and requires >100 nanograms of high-quality genomic DNA (see sample submission).
Example of the distribution of Differentially Methylated Regions (DMRs) obtained with RRBS. Typical percentages in promoters, introns, and exons are shown.
This section is currently under construction.