Expression profile in response to salt-treatment in wheat
ABSTRACT: This SuperSeries is composed of the following subset Series: GSE8060: Expression profile in response to salt-treatment in wheat using 22k microarray GSE8064: Expression profile in response to salt-treatment in wheat using 11k wheat array Refer to individual Series
Project description:Analysis of transcripts in response to salt treatment. In order to design the 22k wheat oligo-DNA microarray, a total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multi-step selection of the sense strand, 21,939 60-mer oligo DNA probes were selected for attachment on the microarray slide. This 22k oligo DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than two-fold in response to salt. These included genes known to mediate the response to salt as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription (RT)-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in the response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo DNA microarray is a reliable method for monitoring global gene expression patterns in wheat. Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.Each experiment was design for comparison in control and treated sample.
Project description:Global expression analysis of transcripts in response to salt treatment was carried out for common wheat using oligo-DNA microarrays. Microarrays have been designed from unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of common wheat were treated with 150 mM NaCl for 1, 6 and 24 hours and their roots and shoots were separately subjected to microarray analyses. Consequently, 5996 genes showed changes in expression of more than two-fold, and were classified into 12 groups according to correlations in gene expression patterns. These salt-responsive genes were assigned functions using Gene Ontology (GO) terms. Genes assigned to transcription factor, transcription-regulator activity and DNA binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data on gene expression suggest that multiple signal transduction pathways in response to salt treatment exist in wheat. Salt-responsive transcription factors (TFs), namely AP2/EREBP, MYB, NAC and WRKY, were selected and their expression patterns compared with those of rice. Most showed different expression patterns in wheat and rice in response to salt treatment. Furthermore, comparing the microarray data for wheat and rice, only a small number of genes were up- or down-regulated in common in response to salt treatment. These findings suggest that salt-responsive mechanisms distinct from rice might be present in wheat, and wheat genes can contribute to providing novel gene resources for breeding of salt-tolerant crops. Microarray hybridization was performed by a competitive two-color method including color-swap experiments. Chinese Spring wheat was grown for two weeks and treated with 150mM NaCl for 0, 1, 6 and 24 hours. RNA samples were extracted from roots and shoots.
Project description:Transcription factors encoded by GLK genes are putative positive regulators of chloroplast development. To identify the potential downstream genes regulated by OsGLK1, we performed the rice 44k oligo microarray analysis. Keywords: over-expression of full-length cDNAs Total RNA was extracted from calluses derived from T1 seeds of the OsGLK1 full length cDNA overexpression line and the control line grown on the N6D medium with 30 mg/l of Hyg for 14 days at 30˚C, and subjected to 44k oligo-DNA microarray with 4 biological replicates.
Project description:Profiles of gene expression in hepatopancreas isolated from shrimp experimentally infected with White Spot Syndrome Virus were compared to those of un-infected controls Keywords: response to viral disease Two groups of eight shrimp were compared in terms of hepatopancreas gene expression, 40 hours after challenge with White Spot Syndrome Virus
Project description:To summarize the impact of high temperature on rice grain filling, we performed the rice 44k oligo microarray analysis. Total RNA was extracted from developing caryopses ripened under 33˚C/28˚C (high temperature) and 25˚C/20˚C (Control), and subjected to 44k oligo-DNA microarray with 3 biological replicates.
Project description:In the japonica rice strain Gimbozu EG4, the DNA transposon mPing is actively transposing to attain over 1,000 copies, whereas in Nipponbare, where this element is virtually silent and has only 50 copies. To analyze the impact of such a massive amplification of transposable element on gene regulation, we performed the rice 44k oligo microarray analysis. Total RNA was extracted from 7-day-old seedlings of EG4 and Nipponbare plants, grown in a greenhouse at at 26˚C and subjected to 44k oligo-DNA microarray with 4 biological replicates.
Project description:A microarray analysis of wheat grain hardness For both the Heron and Falcon NIL, whole wheat heads were harvested at 6, 15 and 25 days post anthesis (DPA) from glass house grown material and stored at -80 OC. For the other wheat cultivars analysed, heads at approximately 9-10 DPA were used. Eight to ten developing caryopses at the same age and morphological stage of development were selected from a head to represent a sample. Seed collected from a different head represented a replicate sample. Total RNA was isolated from the whole seed following the method of Higgins et al. (1976) with the following modification to remove starch. After the lithium chloride precipitation, the RNA pellet was resuspended in 250 ?l water. Then 3.5 ?l of 3 M sodium acetate (pH 5.3) and 125 ?l ethanol were added and the sample was centrifuged for 10 minutes at 4 OC. The supernatant was transferred to a fresh tube and the RNA was ethanol-precipitated by the addition of 21.5 ?l of 3 M sodium acetate (pH 5.3) and 375 ?l ethanol. The recovery of RNA varied from 0.06-0.5 ?g RNA per mg of tissue and this was dependent on the developmental stage of the seeds used for extraction of the RNA. For the labelling procedure, 50 ?g of total RNA was used for both the Cy3 and Cy5 dyes (Amersham Pharmacia, UK), following the two-step labelling method of Schenk et al. (2000). The Cy3 control (hard wheat) and Cy5 sample (soft wheat) were swapped among the replicate experiments to minimise any bias in cDNA incorporation and photo-bleaching of the fluorescent dyes. The pre-hybridisation of the microarray slides, hybridisation of the target cDNA and subsequent washing of the slides to remove unbound target was performed as per the supplied protocol for the CMT-GAPSTM coated microscope slides (Corning USA). The slides were scanned with a GenePix 4000A microarray scanner (Axon Instruments, Union, CA, USA). The features were analysed using the GenePix Pro 4 software and unsatisfactorily segmented features were either manually adjusted or discarded to ensure the integrity of the data obtained.
Project description:Experiment designed to identify differences in gene expression profile in white adipose tissue upon stimulation by beta 3 adrenergic receptor agonist. This series compares 2 groups of C57BL/6J acutely treated with CL-316,243 or Saline for 3 hours.
Project description:Effect of human macrophages phagocytosis on the global transcriptome of EDL933 at different time. Infection of THP-1 with EDL933. Application of SCOTS technique to have cDNA. Hybridation on microarray. Reference: EDL933 in RPMI medium Keywords: stres response, host-bacteria response, time-course For each time point, 2 microarray are analysed and on each microarray there is 2 replicate Total of 4 replicate for each time point (including reference medium)
Project description:Resistance to agricultural fungicides in the field has created a need for discovering fungicides with new modes of action. DNA microarrays, because they provide information on expression of many genes simultaneously, could help to identify the modes of action. To begin an expression pattern database for agricultural fungicides, transcriptional patterns of Saccharomyces cerevisiae strain S288C genes were analysed following 2-h treatments with I50 concentrations of ergosterol biosynthesis inhibitors commonly used against plant pathogenic fungi. Eight fungicides, representing three classes of ergosterol biosynthesis inhibitors, were tested. To compare gene expression in response to a fungicide with a completely different mode of action, a putative methionine biosynthesis inhibitor (MBI) was also tested. Expression patterns of ergosterol biosynthetic genes supported the roles of Class I and Class II inhibitors in affecting ergosterol biosynthesis, confirmed that the putative MBI did not affect ergosterol biosynthesis, and strongly suggested that in yeast, the Class III inhibitor did not affect ergosterol biosynthesis. The MBI affected transcription of three genes involved in methionine metabolism, whereas there were essentially no effects of ergosterol synthesis inhibitors on methionine metabolism genes. There were no consistent patterns in other up- or downregulated genes between fungicides. These results suggest that inspection of gene response patterns within a given pathway may serve as a useful first step in identifying possible modes of action of fungicides. agricultural sterol biosynthesis inhibitor fungicides. Keywords = agriculture Keywords = ergosterol Keywords = methionine Keywords = fungicide Keywords = Saccharomyces cerevisiae S288C Keywords = biosynthesis