Protocols

Genome-wide enrichment of endogenous DNA from non-invasive samples from Snyder-Mackler et al

     Protocol for RNA bait generation

     Protocol for hybridization and library prep

Software and tools

Mixed model Association for Count data via Augmentation from Lea, Tung, and Zhou

     MACAU (binomial mixed model with kinship/population structure controls, for bisulfite sequencing studies) is maintained by our collaborator Xiang Zhou (University of Michigan Biostatistics). You can download the software and user manual here.

WHODAD from Snyder-Mackler et al.

     WHODAD (software for paternity assessment and pedigree ascertainment from low coverage resequencing data) is maintained by our collaborator Xiang Zhou (University of Michigan Biostatistics). You can download the software and user manual here.

Bisulfite sequencing simulator/power analysis (R Shiny app from Lea et al, forthcoming)

     This R Shiny app interactively simulates bisulfite sequencing read counts and performs power analysis using a variety of common modeling approaches for DNA methylation analysis. You can download the app, example input files, and instructions here, or the instructions/readme file on its own here.

     If you use this app in published work, please cite: Lea, A.J., Vilgalys, T.P., Durst, P.A.P., and Tung, J. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. bioRxiv: dx.doi.org/10.1101/091488

Genome-wide quantification of the effects of DNA methylation on gene regulation (mSTARR-seq) from Lea et al.

     Complete protocol

     

     *The mSTARR-seq CpG-free plasmid, pmSTARRseq is also available upon request. Because part of the pmSTARRseq is based on Invivogen's pCpGfree-promoter-Lucia plasmid, it can only be distributed under a Limited Use License to scientific collaborators, provided that the transfer is not for any commercial purpose and pending agreement in writing (a) not to transfer the vector or derivatives to any third party, and (b) to use the vector solely for research and not for commercial purposes. If you wish to obtain this vector, please sign the corresponding declaration and return it by e-mail to Tawni Voyles along with your request.

Tung lab reduced representation bisulfite sequencing (RRBS) protocol