Gene expression profile in rice developing caryopsis exposed to high temperature
ABSTRACT: 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: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: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:Normal, premalignant and various histological subtypes of testicular germ cell tumor (TGCT) tissues were hybridized against Universal Human Reference RNA (Stratagene) onto Agilent 60mer oligo microarrays (GEO accession no GPL885). In vitro time series of two TGCT cell lines, NTERA2 and 2102Ep, treated with retinoic acid for 0, 3, and 7 days were also included. The data set (30 hybridizations) is particularly useful for comparisons between various histological subtypes of TGCT versus each other or versus normal testis.<br><br>Data were imported from their GEO record, which contains no information about which dyes were scanned in which channels. CH1 and CH2 have therefore been used throughout.
Project description:Wood is one of the most important and enormous biomass that is widely used in our life. It is formed by successive addition of secondary xylem that develops continuously from cambium. The transcriptome of nst1 nst3 “double-knockout” lines was examined to know the effect of mutations on wood formation. Experiment Overall Design: Total RNA was extracted from the base 4 cm part of inflorescence stems whose heights were between 12 and 17 cm of three independent nst1-1 nst3-1 double T-DNA tagged lines and the whole transcriptome was compared with that of wild-type plant.
Project description:ER bodies are endoplasmic reticulum (ER)-derived organelles that might be involved in defense systems. The NAI1 gene regulates the development of ER bodies because mutation of NAI1 abolishes the formation of ER bodies. The nai1-1 mutant had a single nucleotide change at an intron acceptor site of At2g22770 (NAI1 gene). Because of this mutation, aberrant splicing of NAI1 mRNA occurs in the nai1-1 mutant. NAI1 encodes a transcription factor that has a basic-helix-loop-helix (bHLH) domain. Transient expression of NAI1 induced ER bodies in the nai1-1 mutant. To identify genes that are related to ER bodies, we compared the genome-wide expression profiles of Col-0 and the nai1-1 mutant using DNA microarrays. Twenty-nine genes were found to be expressed at least 2-fold more strongly in the nai1-1 mutant than in Col-0, and 341 genes were found to be expressed at least 2-fold more strongly in Col-0 than in the nai1-1 mutant. The 15 genes that showed the strongest expression in Col-0 compared to the expression in nai1-1 are shown in Table 1. Five of these genes are JAL genes (JAL22, JAL23, JAL31, JAL33 and PBP1/JAL30). The mRNA level of PYK10 was reduced in nai1-1 (4.3 fold larger in Col-0 than in nai1-1). The mRNA levels of GLL genes (GLL23 and GLL25) were also reduced in nai1-1. Experiment Overall Design: Total RNA was purified from the roots of 20-day-old plants (3 plants were pooled for each genotype). Arabidopsis plants were grown under continuous light condition at 22˚C on MS medium paltes. The control plants and the nai1-1 mutant were cultivated in the same plate. This was done to avoid any difference in plant growth conditions between the mutants and the control plants.
Project description:The loss-of-function mutation of the RGE1 (retarded growth of embryo) gene, which is expressed during seed development, caused small and shriveled seeds. The embryo of the loss-of-function mutant showed retarded growth after the heart stage although abnormal morphogenesis and pattern formation of the embryo and endosperm was not observed. RGE1 expression was determined in endosperm cells using the β-glucuronidase reporter gene and RT-PCR. The differences of expression profile between rge1-1 and wild type Col-0 was examined to know the functions of RGE1. The result of Microarray analysis showed specific down-regulation of putative GDSL motif lipase genes in the rge1-1 mutant indicating possible involvement of these genes in seed morphology. Experiment Overall Design: Total RNA was isolated from siliques of rge1-1 and wild type at 12 DAF using an RNAqueous Kit (Ambion, Inc, USA).
Project description:CAF-1 is involved in nucleosome assembly following DNA replication and nucleotide excision repair. In Arabidopsis thaliana, the 3 CAF-1 subunits p150, p60 and p48 are encoded by FAS1, FAS2 and, most likely, MSI1, respectively.fas mutants exhibited increased levels of DNA double-strand breaks, a G2 phase retardation, and elevated levels of mRNAs coding for proteins involved in homologous recombinational repair. The same genes that were transcriptionally up-regulated in the fas mutants were also found to have a higher steady state level of transcription in wild-type Arabidopsis plants exposed to gamma-irradiation. Experiment Overall Design: Total RNA prepared from 4-week-old seedlings (without the roots i.e. true leaves with cotyledon and hypocotyls) using an RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Four-week-old sterile seedlings of wild-type plants (ecotype Nossen) were irradiated with 100 Gy of gamma-rays at a dose rate of 300 Gy/h. Six and 12 hours after irradiation, samples were frozen in liquid nitrogen and immediately ground for total RNA isolation. After confirming its quality, extracted RNA was prepared for microarray analysis. An Arabidopsis 2 Oligo Microarray kit (Agilent Technology, CA, USA) was used in this study. After confirming its quality, extracted RNA was prepared for microarray analysis as described by the manufacturer (Agilent) using the suggested chemicals and reagents.
Project description:We generated more than 23,000 independent Arabidopsis transgenic lines that expressed rice fl-cDNAs (Rice FOX Arabidopsis lines). The short generation time and rapid and efficient transformation frequency of Arabidopsis enabled the functions of the rice genes to be analyzed rapidly. We screened rice FOX Arabidopsis lines for alterations in morphology, photosynthesis, element accumulation, pigment accumulation, hormone profiles, secondary metabolites, pathogen resistance, salt-tolerance, UV signaling, high light tolerance, and heat stress tolerance. Since we isolated 6 genes (AK069096, AK073112, AK073675, AK065297, AK102323 and AK073210) causing an increase in the abundance of metabolites or pigments detected by absorption data, we investigated the expression profiles in transgenic plants by using microarray analysis. Expression of the genes encoding chalcone synthase and dihydroflavonol-4-reductase was increased in all 6 cDNA transformants. These results indicate that an increase in expression of the genes encoding flavonoid biosynthesis enzymes caused an accumulation of pigments in these 6 transformants. Experiment Overall Design: Total RNA was isolated from aerial parts of re-transformants of some rice cDNAs and wild type using an RNAqueous Kit (Ambion, Inc, USA).
Project description:In plants, secondary wall thickenings play important roles in various biological processes, although the factors regulating these processes remain to be characterized. We show that expression of chimeric repressors derived from NAC SECONDARY WALL THICKENINGS PROMOTING FACTOR1 (NST1) and NST2 in Arabidopsis resulted in an anther dehiscence defect due to loss of secondary wall thickening in anther endothecium. Plants with double, but not single, T-DNA-tagged lines for NST1 and NST2, had the same anther-indehiscent phenotype as transgenic plants that expressed the individual chimeric repressors, indicating that NST1 and NST2 are redundant in regulating secondary wall thickening in anther walls. The activity of the NST2 promoter was particularly strong in anther tissue, while that of the NST1 promoter was detected in various tissues in which lignified secondary walls develop. Ectopic expression of NST1 or NST2 induced ectopic thickening of secondary walls in various above-ground tissues. Epidermal cells with ectopic thickening of secondary walls had structural features similar to those of tracheary elements. However, among genes involved in the differentiation of tracheary elements, only those related to secondary wall synthesis were clearly upregulated. None of the genes involved in programmed cell death was similarly affected. Our results suggest NAC transcription factors as possible regulators of secondary wall thickening in various tissues. Experiment Overall Design: Total RNA was extracted from rosette leaves of two independent 2-week-old T1 plants over-expressing NST1 driven by 35S promoter and the whole transcriptome was compared with that of wild-type plant.
Project description:Decreasing oocyte competence with maternal aging is a major factor in human infertility. To investigate the age-dependent molecular changes in a mouse model, we compared the expression profiles of metaphase II oocytes collected from 5-6 week old mice with those collected from 40-42 week old mice using the NIA 22K 60-mer oligo microarray.