The Mouse Universal Genotyping Array: From Substrains to Subspecies.

Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content of GigaMUGA is optimized for genetic mapping in the Collaborative Cross and Diversity Outbred populations, and for substrain-level identification of laboratory mice. In addition to 141,090 single nucleotide polymorphism probes, GigaMUGA contains 2006 probes for copy number concentrated in structurally polymorphic regions of the mouse genome. The performance of the array is characterized in a set of 500 high-quality reference samples spanning laboratory inbred strains, recombinant inbred lines, outbred stocks, and wild-caught mice. GigaMUGA is highly informative across a wide range of genetically diverse samples, from laboratory substrains to other Mus species. In addition to describing the content and performance of the array, we provide detailed probe-level annotation and recommendations for quality control.

Mechanical tissue optical clearing technique increases imaging resolution and contrast through ex vivo porcine skin.

BACKGROUND AND OBJECTIVES: Mechanical tissue optical clearing permits light delivery deeper into turbid tissue, which may improve current optical diagnostics and laser-based therapeutic techniques. We investigated the effects of localized compression on brightfield imaging through ex vivo porcine skin by evaluating resolution and contrast of a target positioned beneath native, mechanically compressed, or chemically cleared specimens. We also evaluated the effects of indentation on dynamic tissue thickness and light transmission. STUDY DESIGN/METHODS: A 5 mm diameter, hemispherically tipped, manual load transducer was used to compress specimens using 2-44 N for 60 seconds. Chemically cleared specimens were immersed for 1 hour in glycerol or dimethyl sulfoxide. A USAF 1951 resolution target was positioned beneath specimens and imaged using brightfield microscopy. Resolution and contrast of target features were analyzed. In separate experiments, a mechanical test instrument was used to compress and hold specimens at a final thickness while measuring applied load and light transmission. RESULTS: Image intensity profiles showed that while uncompressed skin did not allow resolution of any target, localized compression allowed maximum resolution up to a line width of 173 ± 21 µm. Mechanical clearing achieved up to four times higher maximum resolution and 2-3 times higher contrast sensitivity than chemical immersion. Resolving capability was highly correlated with compressive tissue strain. Light transmission increased during tissue compression, but also increased while holding final thickness constant. CONCLUSION: Localized compression is an effective technique for increasing resolution and contrast of target features through tissue and may improve light-based diagnostics. Thickness reduction and other mechanisms appear to contribute to this effect.