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GSE15971
Arabidopsis thaliana
6 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Pollen is the male gametophyte of land plants. Proper development and maturation of pollen is necessary for the successful reproduction of seed plants. This process involves sophisticated coordination between sporophytic and gametophytic tissues in anthers. To advance the mechanistic studies of anther development, additional players need to be discovered for a comprehensive understanding of the underlying regulatory network. Here we show that the Arabidopsis dual specificity tyrosine phophorylated and regulated kinase (DRYK), AtYAK1, is essential for development of rosette leaves and the male but not female gametophyte in Arabidopsis. Arabidopsis mutant plants carrying a mutation in AtYAK1 produce developmentally stalled microspores, likely because of the defects in the two consecutive mitosis steps in the post-meiotic maturation process of pollen. The mutation of AtYAK1 has a significant effect on gene expression programs in developing pollen. Transcritpome analysis of atyak1 revealed downstream genes in families of protein kinases, transporters and transcription factors, which potentially contribute to pollen development. This study represents the first molecular characterization of DYRK in the plant kingdom. Our results also imply that the regulation of cytokinesis by DYRKs is evolutionally conserved in fungus, fruit fly, animals and plants.
Publication Title
No associated publication
Sample Metadata Fields
Age, Specimen part
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Transcriptome analysis has revealed a light-regulated WD (tryptophan and aspartate)-containing protein, LWD1. LWD1 and LWD2 share greater than 90% amino acid sequence homology. The lack of phenotype changes in the lwd1 or lwd2 single mutant implies that the proteins function redundantly. The lwd1lwd2 double mutant, however, has an early flowering phenotype under both long-day (LD) and short-day (SD) conditions. Functional complementation experiment revealed that LWDs are indeed responsible for the defect in photoperiod sensing in lwd1lwd2 double mutant plants. The expression of LWD1 exhibits a diurnal pattern and peaks before dawn. The period length of oscillator (CCA1, LHY, TOC1 and ELF4) and output (CCR2 and CAB2) genes in the lwd1lwd2 double mutant is significantly shorter than that in wild-type Arabidopsis under free running condition. Under entrainment conditions, the expression phase of oscillator (CCA1, LHY, TOC1 and ELF4) and output (GI, FKF1, CDF1, CO and FT) genes shifts ~3 hr forward in the lwd1lwd2 double mutant. Our data indicated that the early flowering phenotype in lwd1lwd2 plants is contributed by the significant phase shift of CO and, therefore, an increased expression of FT before dusk under SD conditions. Our data imply that LWD1/LWD2 proteins function in close proximity to the circadian oscillators for the regulation of photoperiod sensing.
Publication Title
Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering.
Sample Metadata Fields
No sample metadata fields
View Samples- Arabidopsis thaliana
- 4 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis emf2 mutants bypass vegetative development and flowering upon seed germination. We introduced a broccoli BoEMF2.1 gene into emf2 mutants and obtained rescued emf2 plants that harbored 35S::BoEMF2.1. We found that BoEMF2.1 can partially rescue the phenotype of emf2 to that of WT. We used microarrays to study the global program of gene expression and to identify genes misexpressed in the Arabidopsis emf2 mutant that had been rescued by 35S::BoEMF2.1.
Publication Title
Molecular and functional characterization of broccoli EMBRYONIC FLOWER 2 genes.
Sample Metadata Fields
Age, Specimen part
View Samples- Glycine max
- 6 Downloadable Samples
Illumina HiSeq 2000
Description
To understand the function of soybean endosperm
Publication Title
No associated publication
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 22 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Due to limited bio-availability of Fe, plants evolved adaptive alterations in development regulated at the transcriptional level. We investigated the early transcriptional response to Fe deficiency.
Publication Title
Early iron-deficiency-induced transcriptional changes in Arabidopsis roots as revealed by microarray analyses.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
The environmental light plays a vital role in regulating the plant growth and development. Transcriptomic profilings were widely used to examine how light regulates the changes of mRNA populations at a genome-wide scale. However, it remains unclear if translational regulation represents a new dimension of gene expression regulation in response to the light signal. Through a transcriptomic comparison of steady-state and polysome-bound mRNAs, we revealed an increased translational efficiency in de-etiolating Arabidopsis seedlings. Over 3,500 genes are subjected to translational regulation whereas only about 770 genes have increased mRNA abundances in response to the light signal. This result suggests a stronger impact of translational control over transcriptomic changes during photomorphogenesis. Genes encoding ribosomal protein are preferentially regulated at the translational level, possibly contributing to the enhancement of translation efficiency as observed. We also uncovered mRNAs regulated at the translational level share characteristics of longer half-lives and shorter cDNA length. The presence of a cis-element, TAGGGTTT, in the 5untranslated region of a transcript renders its translational regulation by light signals. Taken together, our study revealed a previously neglected aspect of gene expression regulation during Arabidopsis photomorphogenesis. The identities and molecular signatures associated with mRNAs regulated at the translational level also offer new directions to perform mechanistic studies of light-trigged translational enhancement in Arabidopsis.
Publication Title
Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis.
Sample Metadata Fields
Specimen part, Treatment, Time
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
CsUBC13 was identified via proteomics from iron starvation treated Cucumber root. ubc13A is an ABRC seed stock (CS51269). CS851269 was purchased from ABRC and confirmed as homozygous Atubc13A knock-out T-DNA mutant. We generated transgenic arabidopsis with ectopic expression of CsUBC13 gene under control of the cauliflower 35S promotor. Both genotypes and Col-0 were used to investigate the transcriptional response to Iron (Fe) deficiency.
Publication Title
A lysine-63-linked ubiquitin chain-forming conjugase, UBC13, promotes the developmental responses to iron deficiency in Arabidopsis roots.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 18 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
We have reported that JMJ17 act as a repressor to a set of genes involved in photosynthesis, tetrapyrrole biosynthesis and light response related development in the dark, while during dark to light irradiation it acts as an activator of same set of genes.
Publication Title
No associated publication
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 16 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Plants can be primed by a stress cue to mount a faster and stronger activation of defense mechanisms upon a subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress, a phenomenon known as transcriptional memory. The transcriptional memory in response to heat stress is not clear at the genome scale.
Publication Title
Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Pluripotent stem cells, including human embryonic stem (hES) and induced pluripotent stem (hiPS) cells, have been regarded as useful sources for cell?based transplantation therapy. However immunogenicity of the cells remains the major determinant for successful clinical application. We report the examination of several hES cell lines (NTU1 and H9), hiPS cell lines, and their derivatives (including stem cell?derived hepatocytes) for the expression of major histocompatibility complex (MHC), natural killer (NK) cell receptor (NKp30, NKp44, NKp46) ligand, immune?related genes, human leukocyte antigen (HLA) haplotyping, and the effects in functional mixed lymphocyte reaction (MLR). Flow cytometry showed lower levels (percentages and fluorescence intensities) of MHC class I (MHC?I) molecules, 2?microglobulin and HLA?E in undifferentiated stem cells, but the levels were increased after co?treatment with interferon gamma and/or in vitro differentiation. Antigen presenting cell markers (CD11c, CD80 and CD86) and MHC?II (HLA?DP, DQ and DR) remained low throughout the treatments. Recognitions of stem cells/derivatives by NK lysis receptors were lower or absent. Activation of responder lymphocytes was significantly lower by undifferentiated stem cells than by allogeneic lymphocytes in MLR, but differentiated NTU1 hES cells induced a cell number?dependent lymphocyte proliferation comparable with that by allogeneic lymphocytes. Interestingly activation of lymphocytes by differentiated hiPS cells or H9 cells became blunted at higher cell numbers. Real?time RT?PCR showed significant differential expression of immune privilege genes (TGF?2, Arginase 2, Indole 1, GATA3, POMC, VIP, CALCA, CALCB, IL?1RN, CD95L, CR1L, Serpine 1, HMOX1, IL6, LGALS3, HEBP1, THBS1, CD59 and LGALS1) in pluripotent stem cells/derivatives when compared to somatic cells. It is concluded that pluripotent stem cells/derivatives are predicted to be immunogenic, though evidences suggest some levels of potential immune privilege. In addition, differential immunogenicity may exist between different pluripotent stem cell lines and their derivatives
Publication Title
Characteristic expression of major histocompatibility complex and immune privilege genes in human pluripotent stem cells and their derivatives.
Sample Metadata Fields
Sex, Specimen part
View Samples