Project description:Investigation of gene expression level changes in evolved polygamous and monogamous populations of Drosophila melanogaster. The populations investigated are described in Hollis et al. 2011. Populations with elevated mutation load do not benefit from the operation of sexual selection. Journal of Evolutionary Biology 24: 1918-1926. A study using total RNA extracted from male and female virgin 4-day old Drosophila melanogaster and then transcriptionally profiled with 12x135k Nimblegen arrays. Also, transcriptional profiling of male and female heads from the same populations using Illumina RNA-Seq.
Project description:Study of transcriptome level changes in Drosophila melanogaster populations with divergent reproduction and lifespan patterns A 120 chip study using mRNA recovered from unmated female fruit flies 35 generations after selection for contrasting life history traits. The study includes samples from five age classes and two tissues of flies derived from three replicated populations.
Project description:The data explore the transcriptional response of strains LY180 and EMFR9 to 5 mM furfural under anaerobic fermentation condition The data explore the transcriptional response of strains LY180 and EMFR35 to 15 mM furfural under anaerobic fermentation condition The expression differences of polyamine transporters in LY180 vs EMFR9 and EMFR35 are further described in RD Geddes,X Wang, LP Yomano, EN Miller, H Zheng, KT Shanmugam, and LO Ingram. 2013. Selected Polyamines and Polyamine Transporters Increase Furfural Tolerance (in preparation for submission to Appl Env Microbiol) Total RNA was prepared from cultures of LY180, EMFR9 and EMFR35 immediately before and 15 min after addition of furfural (5mM and 15 mM). The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene. The complete dataset comprising 8 samples is linked below as a supplementary file.
Project description:Investigation of genome-wide gene expression in sepals, petals, stamens, staminodia and carpels in pre-anthesis Aquilegia flowers. One goal was to identify transcriptional signatures associated with petaloidy by comparing gene expression in petals and petaloid sepals. Other goals were to study the evolutionary origin and ecological function of staminodia by comparing a) expression patterns in stamens, staminodia and carpels, b) identifying transcriptional regulators expressed in staminodia and c) using gene set enrichment analysis to identify biological processes operating in staminodia. A 15 chip study using total RNA from the five floral tissues from three replicate natural populations with each sample representing tissue pooled from 60 flowers.
Project description:We compare gene expression among petals tissues in 5 species of natural allotetraploid and F1 hybrid cottons to the antecedent conditions existing prior to genome merger and duplication, thus revealing the effects of genome merger and polyploidy on gene expression evolution 27 total samples, including 3 reps. each of five natural tetraploid species, a F1 hybrid, two parental species, and a 1:1 RNA mix of the parental species
Project description:We explored the transcriptomic alterations associated with domestication by interrogating a developmental time course of cotton fibers from the wild G. hirsutum var. yucatanense and a representative of an elite domesticated line. 30 chip design - including 2 species (wild and domesticated cotton), by 1 tissue (fiber), for 5 timepoints (2,7,10,20, and 25 days after anthesis), with 3 replicates per timepoint
Project description:Universally accepted landmark stages are necessary to highlight key events in tomato reproductive development. In this study, we provide a description of floral and fruit development in a red-fruited closely related wild relative of tomato, Solanum pimpinellifolium accession LA1589. We use established and propose new landmarks as the framework for the characterization of the tomato fruit shape gene SUN in fruit development. SUN controls fruit shape predominantly after fertilization and its effect reaches a maximum at 8 days post anthesis coinciding with fruit landmark 4 representing the globular embryo stage of seed development. We also analyzed gene expression profiles of floral buds 10 days before anthesis (floral landmark 7), anthesis-stage flowers (floral landmark 10 and fruit landmark 1), and 5 days post anthesis fruit (fruit landmark 3). The expression profiles of the NILs that differ at sun showed that 34 genes were differentially expressed and most of them at a less than 2-fold difference. However, many genes were differentially expressed between the developmental times points, including many genes involved in phytohormone biosynthesis or signaling as well as organ identity and patterning of tomato fruit. Three biological replicates were conducted with three sets of LA1589 sun NILs that differ at sun growing during different time periods resulting in 3 time points x 2 genotypes x 3 replicates = 18 array hybridizations.
Project description:The data explore the transcriptional response of strain LY180 to 15 mM furfural under anaerobic fermentation conditions. The expression differences of oxidoreductase in LY180 are described. Total RNA was prepared from cultures of LY180 immediately before and 15 min after addition of furfural to 15 mM. The NimbleGen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.
Project description:Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for serum resistance. 4-plex array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri exposed to heat-inactivated catfish serum and normal serum. Each treatment had four biological replica and each plex had two probe sets.
Project description:Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for host encounter. 4-plex NimbleGen array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri encountered with or without catfish fry. Each treatment had four biological replica and each plex had two probe sets.