Project description:Analysis of loss-of-function mutants of JUMONJI30 (JMJ30) and JMJ32 in Arabidopsis thaliana (Col). JMJ30 and JMJ32 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 and JMJ32 encode H3K27me3 demethylases, and genes down-regulated in jmj30 jmj32 mutant are enriched for H3K27me3 targets. Columbia wild-type (Col WT) and jmj30 jmj32 mutant were grown at 29°C, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and jmj30 jmj32 seedling mRNA samples were used for this array.
Project description:Analysis of overexpression of JMJ30 in Arabidopsis thaliana (Col). JMJ30 encode the histone demethylases that contain the catalytic JmjC domain. The trimethylation of Histone H3 lysine 27 (H3K27me3) plays a key role in gene repression and developmental regulation. It is actively and dynamically deposited and removed in plants. However, while the H3K27 methyltransferases had been extensively studied, findings on the H3K27 demethylase were few. Here, we show that JMJ30 encodes a H3K27me3 demethylase, and genes up-regulated in 35S::JMJ30-HA transgenic lines are enriched for H3K27me3 targets. Columbia wild-type (Col WT) and 35S::JMJ30-HA transgenic plants were grown at 22°C under long day conditions, and seedling samples were collected at 13 day-after-germination (DAG). Two independent sets of WT and 35S::JMJ30-HA seedling mRNA samples were used for this array.
Project description:Investigation of the effect of the knockdown of AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background Transposable elements (TEs) are silenced by epigenetic mechanisms of DNA and histone methylation. The repressive histone modification H3 lysine 9 dimethylation (H3K9me2) is TE-associated epigenetic hallmark, and is necessary for DNA methylation. However the mechanism to direct the repressive epigenetic modification in TEs has remained elusive. Here we show that knockdown of the AT-hook motif DNA binding nuclear matrix protein TRANSPOSABLE ELEMENT KILLER (TEK) in the Arabidopsis Landsberg erecta (Ler) background results in robust activation of various TEs, the repeat-containing floral repressor gene FWA and the TE-containing floral repressor FLOWERING LOCUS C (FLC). A four chip study using two separate wild-type seedling mRNA samples and two separate TEKi seedling mRNA samples
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:Mesorhizobium huakuii 7653R is an M-NM-1-proteobacterium that occurs either in a nitrogen-fixing symbiosis with its host plant, A. sinicus, or free-living in the soil. Investigation of whole genome gene expression level changes in Bacteroids compared to the free-living cells. Understand how M. huakuii 7653R responds to alterations in its environment and to the physiological changes that occur during bacteroid differentiation. Examination of mRNA levels in free-living cells and bacteroids at 32 days postinoculation
Project description:Investigation of the phylogenetic diversity of Acidobacteria taxa using PCR amplicons from positive control 16S rRNA templates and total genomic DNA extracted from soil and a soil clay fraction A ten chip study using PCR amplicons from cloned 16S rRNA genes and from diverse soil 16S rRNAs, with PCR primers specific to the Division Acidobacteria. Each chip measures the signal from 42,194 probes (in triplicate) targeting Acidobacteria division, subdivision, and subclades as well as other bacterial phyla. All samples except one (GSM464591) include 2.5 M betaine in the hybridization buffer. Pair files lost due to a computer crash.
Project description:Investigation of expression differences between melanomas harvested from MiniCoopR-GFP versus MiniCoopR-SETDB1 transgenic zebrafish. An eight-chip study using total RNA prepared from four distinct melanomas from zebrafish injected with MiniCoopR-GFP (control) transposon and four distinct melanomas from zebrafish injected with MiniCoopR-SETDB1 transposon. Injected animals carried a p53 loss-of-function mutation, a mutation in nacre, and an mitf:BRAF-V600E transgene. Each chip measures the expression level of 32,292 genes.
Project description:Investigation of whole genome transcription expression level changes in Drosophila mojavensis wild-type populations (1. Punta Onah:PO; 2. Organ Pipe National Manument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ). The experiment was designed to investigate effects of desiccation exposure (0, 9 & 18 hr) and host plant (diet) on transcriptome. A total of 95 hybridizations were performed in this entire experiment. We used 135K 12-plex NimbleGen arrays. Total RNA was recovered from each sample listed below. The experimental design consisted a total of four populations (1. Punta Onah:PO; 2. Organ Pipe National Manument:OPNM; 3. Punta Prieta:PP; & 4. San Quintin:SQ), two host diets (Agria and Organ pipe) and three desiccation treatments (0, 9 and 18 hours). Each chip measures the expression level of 15528 transcripts. Four to 5 replicates were used for each type (R-1, R-2, R-3 etc.)
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.