Protocols & Data

Protocols

  • Double Digest Genotyping-by-Sequencing (ddGBS) Protocol
    Double digest genotyping-by-sequencing (ddGBS) is a reduced representation genotyping method for sequencing on the Illumina platform. ddGBS libraries are prepared by digesting gDNA with two restriction enzymes and annealing oligonucleotide adapters to the resulting overhangs. By focusing sequencing efforts onto restriction sites, ddGBS achieves higher coverage than if the entire genome was sequenced at random. This protocol was adapted from the original approach using a single restriction enzyme (Elshire et al. 2011) and is optimized for use in rodents. It details how to construct sequencing libraries using a set of 48 indexed adapters (designed by Grabowski et al. 2014). Specifications vary according to the needs of individual projects. It is strongly recommended to contact the Palmer Lab before use to ensure proper concentrations of all adapter stocks and that sample multiplexing will achieve the desired depth of coverage.
  • M. musculus Glo1 Duplication Genotyping Protocol

Software

  • QTLRel
    QTLRel is an R package for mapping quantitative trait loci (QTLs) in experimental crosses such as advanced intercross lines (AILs) where relatedness among individuals should not be ignored.QTLRel includes functions to estimate background genetic variance components, impute missing genotypes, simulate genotypes, perform a genome scan for quantitative trait loci, and plot the mapping results.
  • breedail
    R code to select breeders from an advanced intercross line so that they minimize inbreeding in the offspring.

 Datasets

MICE

  • G50-56 LGxSM AIL GWAS
    This repository contains genotype, phenotype, and gene expression data for LG x SM AIL mice from generations 50-56. This data is available at the public SRA repository at the following link: PRJNA1007382.
  • cfw-craniofacial-gwas
    QTL mapping for craniofacial morphology traits in Swiss Webster (CFW) mice using GEMMA. Contains genotype & phenotype data and R code to reproduce results of upcoming PLoS Genetics article. This project was a collaboration with Luisa F Pallares and Diethard Tautz, Max Planck Institute for Evolutionary Biology in Germany.
  • lgsmfear
    Demonstration of QTL mapping for fear conditioning traits in LG/J x SM/J mouse advanced intercross line. Contains data and R code to reproduce results of a forthcoming Genetics article.
  • ppi-F1-gwas
    QTL mapping for prepulse inhibition phenotypes in F1 panel derived from common inbred mouse strains using a linear mixed model (GEMMA). Contains data and R code to reproduce results of upcoming GWAS manuscript.

RATS

HUMANS

OTHER SPECIES

  • EKW zebrafish sequence reads on Sequence Read Archive (SRA)
    DNA sequences for zebrafish from genetically diverse outbred strain Ekkwill (EKW). Low-coverage WGS data for 5759 individuals, deep-coverage WGS data for 95 out of 122 founder individuals, and deep-coverage WGS data for 7 out of 5759 progeny individuals as a truth set.

 Patents

WIPO Patent: Methods and Compositions for Inhibiting Glyoxalase 1 (GLO1)
Palmer A, Distler M

Methods and Compositions for Inhibiting Glyoxalase 1 (GLO1)

International Patent Number WO2014/159720

Date Issued: October 2, 2014

Abstract:

Methods and compositions are provided for treating or preventing a neurological disease or disorder using an inhibitor of Glyoxalase 1 (GLO1). In some embodiments, the inhibitor is a small molecule. In certain embodiments, the disease or disorder is a sleep disorder, a mood disorder such as depression, epilepsy, an anxiety disorder, substance abuse, substance dependence or substance such as an alcohol withdrawal syndrome.

Metal‐Binding Pharmacophore Library Yields the Discovery of a Glyoxalase 1 Inhibitor for Potential Treatment of Depression and Related Psychiatric Illnesses.

Tech ID: 31771 / UC Case 2020-039-0

Patent pending

Technology Description:

Researchers at UC San Diego have developed glyoxalase (GLO) modulators and methods for treating anxiety, depression, epilepsy, alcoholism, and other forms of drug abuse in a patient and the associated methods for administering to the subject in need thereof a therapeutically effective amount of a compound. Specifically, the inventors have identified novel molecules that inhibit the enzyme GLO1, which is a Zn2+ -dependent isomerase involved in the detoxification of the glycolytic byproducts methylglyoxal (MG). Methylglyoxal (MG) is a reactive metabolite generated via the degradation of glycolytic intermediates and is capable of forming covalent adducts with proteins and nucleotides that result in advanced glycation end (AGE) products, reactive-oxygen species, and apoptosis.