Project description:Hybridization alters the shape of the genotypic fitness landscape, increasing access to novel fitness peaks during adaptive radiation
Project description:Here we developed a new high-throughput polymorphism detection and genotyping method based on identifying restriction cut site polymorphisms using a microarray platform. We compared the genomes of 20 individual urchins; 10 from the northern part of the species range (Boiler Bay, OR) and 10 from the southern part of the range (San Diego, CA).
Project description:The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Chromosomal anomalies in BIN-67 cells were inferred using the Infinium? genotyping technology with the HumanHap300-Duo Genotyping BeadChip (Illumina, San Diego, CA, USA). This BeadChip contains about 318,000 genetic markers within approximately a 5 kb median SNP spacing. Genotyping and imaging using BeadStudio Data Analysis software (Illumina, San Diego, CA, USA) were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC).
Project description:This study is designed to understand whether Pravastatin (Pra) treatment alters the transcriptome of small intestine after radiation injury. RNA was extracted from 15 Gy abdominal irradiated Gottingen minipigs with PS treatment. A cDNA library was generated using a TruSeq Stranded mRNA sample prep kit (Illumina, San Diego, CA), and transcriptome sequencing was performed using a TruSeq 3000/4000 SBS kit and Illumina sequencer with 101 bp paired-end reads per sample (Macrogen, Seoul, Korea).
Project description:A conditional and isogenic system for APOBEC3B (A3B) induction in T-REx-293 cells. Cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs and subjected to 10 rounds of A3B-eGFP exposure causing 80-90% cell death. Control pools (eGFP) were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. DNA was extracted and subjected to SNP analyses using the Human OmniExpress-24v1-0 BeadChip (Illumina, San Diego, CA). Genotyping was performed using the humanomniexpress_24v1-0_a cluster file.
Project description:Ionizing radiation, released during accidents at nuclear power plants or after atomic bomb explosions, is a potentially serious health threat for the exposed human population. This type of high-energy radiation causes DNA damage including single- and double-strand breaks and induces chromosomal rearrangements and mutations, but it is not known if ionizing radiation directly induces changes in the epigenome of irradiated cells. We treated normal human fibroblasts and normal human bronchial epithelial cells with different doses of gamma-radiation emitted from a cesium 137 (137Cs) radiation source. After a recovery period, we analyzed global DNA methylation patterns in the irradiated and control cells using the methylated-CpG island recovery assay (MIRA) method in combination with high-resolution microarrays. Bioinformatics analysis revealed only a small number of potential methylation changes with low fold-difference ratios in the irradiated cells. These minor methylation differences seen on the microarrays could not be verified by COBRA (combined bisulfite restriction analysis) or bisulfite sequencing of selected target loci. Our study shows that acute gamma-radiation treatment of two types of human cells had no appreciable effect on DNA cytosine methylation patterns in exposed cells. DNA methylation patterns in gamma-irradiated cells and non- treated cells analyzed by microarrays