HPCBio Applications
Other Applications and Services
Please, contact us to discuss how we can be of assistance in achieving your project goals or to receive a quote for your project.
Epigenomics
Methylation Sequencing:
Whole genome methylome analysis involves an enzymatic treatment that identifies two types of DNA modifications: 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC). Alternatively, reduced-representation bisulfite sequencing libraries (RRBS) can be constructed from areas of the genome that have high CpG content. Whole genome methylome libraries are typically sequenced to a depth of 10X to 30X, while RRBS libraries typically capture only 1% of the genome so they need a much lower sequencing depth.
ATAC-Seq, Cut&Run:
We have extensive experience in the construction of these libraries. If you want to make them in your lab, we recommend discussing your application with us prior to library construction to ensure that final libraries will be compatible with the latest sequencing technology.
The critical parameters for these libraries are:
- The input DNA must be sheared to a size between 100bp and 600bp prior to pull down. We get consistent results using Covaris sonicators. Ideal sonication times need to be validated for different cell types and range from 10 min to 35 min. After sonication of a test cell suspension, please purify an aliquot of the cells and run the DNA on a 1% or 2% agarose gel with appropriately sized DNA ladder to confirm that the DNA is between 100bp and 600bp. Longer DNAs do not sequence well are most likely not efficiently enriched.
- After immunoprecipitation, we strongly recommend to confirm enrichment by performing qPCR of positive control regions relative to negative control regions before submitting DNA for library construction. A collection of ChIP-Seq data is available at the encode webpage, where the peaks can be visualized on the genome browser and primers can be designed from your genomic regions of interest. A database of primers for many common targets can be found here.
Workflow Development and Deployment
Metagenomics and Metatranscriptomics
Targeted Amplicon Analysis (16S, ITS, custom)
Grant Support
Custom Analyses
Data Management and Deposition
