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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression in pif3 mutant under dark and in wt under Red 1h and Red 18h

ABSTRACT: PIF3 plays a role as repressor of photomorphogenesis in darkness. To identify PIF3-regulated genes that might be implementing this action, we have performed whole-genome expression analysis in the pif3 mutant. Seeds were surface-sterilized and plated on GM medium without sucrose, stratified at 4ºC in the dark for 4 days, exposed to white light for 3 hours to induce germination, and placed in a growth chamber at 21ºC in darkness for 4 days (D0h) and 4 days and 1 hour (D1h). For Rc treatments seedlings were moved to Rc growth chambers at 21ºC for 1 (R1h) and 18 (R18h) hours.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Elena Monte

PROVIDER: E-GEOD-30030 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Functional profiling identifies genes involved in organ-specific branches of the PIF3 regulatory network in Arabidopsis.

Sentandreu Maria M Martín Guiomar G González-Schain Nahuel N Leivar Pablo P Soy Judit J Tepperman James M JM Quail Peter H PH Monte Elena E

The Plant cell 20111122 11

The phytochrome (phy)-interacting basic helix-loop-helix transcription factors (PIFs) constitutively sustain the etiolated state of dark-germinated seedlings by actively repressing deetiolation in darkness. This action is rapidly reversed upon light exposure by phy-induced proteolytic degradation of the PIFs. Here, we combined a microarray-based approach with a functional profiling strategy and identified four PIF3-regulated genes misexpressed in the dark (MIDAs) that are novel regulators of see ...[more]

PMID: 22108407

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Gene expression in hemera mutants in red light condition

Project description:The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22. Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4d. Seedlings were grown in constant red light (Rc, 10?mol/m2/s) at 21°C for 4d.

2014-06-01 | E-GEOD-43311 | biostudies-arrayexpress

Gene expression in pif3 mutant under dark and in wt under Red 1h and Red 18h

Project description:PIF3 plays a role as repressor of photomorphogenesis in darkness. To identify PIF3-regulated genes that might be implementing this action, we have performed whole-genome expression analysis in the pif3 mutant.

2012-01-03 | GSE30030 | GEO

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress

Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress

Orchestration of floral initiation by APETALA1

Project description:This SuperSeries is composed of the following subset Series: GSE20139: Ath_Agilent_v1_Riechmann array expression profile AP1-GR ap1cal inflorescences - time series (hours) GSE20182: Meyerowitz Lab Arabidopsis Operon Array v4 - 4200A scanner - AP1-GR ap1cal inflorescences - time series (hours) GSE20183: Meyerowitz Lab Arabidopsis Operon Array v4 - 4000B scanner - AP1-GR ap1cal inflorescences - time series (hours) Refer to individual Series

2010-04-02 | E-GEOD-20184 | biostudies-arrayexpress

The ability of VSL#3 to restore the age-related deficit in LTP is associated with changes in brain genes expression

Project description:A deficit in synaptic plasticity is one of the many changes that occurs with age. Specifically the archetypal model of plasticity, long-term potentiation (LTP), is reduced in hippocampus of middle-aged and aged animals. Several factors are likely to contribute to this deficit including morphological changes like a net loss of neurons and loss of synapses with the consequent changes in receptor signalling. However it is also clear that ageing is associated with development of oxidative stress, and also inflammatory stress which is typified by increased activation of microglia. Recent evidence has indicated that probiotics exert anti-inflammatory in the gut. Specifically VSL#3, a proprietary probiotic comprising 8 Gram-positive bacterial strains, decreased markers of inflammation in the colon in an animal model of colitis. We considered that its anti-inflammatory effects might extend to brain and therefore that treatment of aged rats with VSL#3 might attenuate the age-related deficit in LTP. The evidence indicates that LTP was impaired in control-treated aged rats but sustained in aged rats which received VSL#3. This was accompanied by a modest decrease in markers of microglial activation and an increase in BDNF and synapsin . The microarray analysis demonstrated that VSL#3 treatment induces changes also in the expression of some brain genes. four sample groups each representing a certain treatment condition of young or adult male Han Wistar rats

2014-04-02 | E-GEOD-51381 | biostudies-arrayexpress

IFN-M-NM-3-induced iNOS expression in regulatory macrophages prolongs allograft graft survival in fully immunocompetent recipients.

Project description:Mouse monocytes exposed to M-CSF and IFN-M-NM-3 were driven to a suppressor phenotype over a seven day culture period. The resulting regulatory macrophages (M regs) expressed markers distinguishing them from M0-, M1-, and M2-polarised macrophages and monocyte-derived DCs. M regs completely suppressed polyclonal T cell proliferation through an inducibile nitric oxide synthase (iNOS)-dependent mechanism. Additionally, M regs were found to eliminate cocultured T cells in an allospecific fashion. In a heterotopic heart transplant model, a single intravenous administration of 5x10^6 donor-strain M regs prior to transplantation significantly prolonged allograft survival in fully immunocompetent recipients using both the stringent C3H-to-BALB/c and C57BL/6-to-BALB/c strain combinations; this graft-protective effect was alloantigen-specific. M regs from Nos2-deficient mice did not prolong allograft survival, proving that M reg function in vivo is iNOS-mediated and dependent on living cells. Co-treatment with 1 mg/kg/day rapamycin for 10 days post-transplant markedly enhanced the effect of M regs. In untransplanted C57BL/6 recipients, M regs of BALB/c origin were detectable for up to 2 weeks post-infusion. It is concluded that mouse M regs represent a novel, phenotypically distinct subset of tolerogenic macrophages, which resemble human M regs in their derivation, phenotype and in vitro functions. The dataset comprises 36 samples divided into twelve sample groups each representing a certain monocyte/macrophage subtype

2013-12-21 | E-GEOD-32690 | biostudies-arrayexpress

Gene expression in hemera mutants in red light condition

2014-06-01 | GSE43311 | GEO

Meyerowitz Lab Arabidopsis Operon Array v4 - 4200A scanner - AP1-GR ap1cal inflorescences - time series (hours)

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (non-commercial; Meyerowitz Lab Arabidopsis Operon Array v4). Keywords: time course Four sets of biologically independent tissue samples were collect at 0, 2, 4 ,8, and 12 hours after the application of dexamethasone (Dex-; activation of the AP1-GR fusion protein) or a mock solution (Mock-; control). In each of the biological replicates of the time course experiments, all the samples derived from dexamethasone (Dex)-treated plants were labeled with one dye (i.e., Cy3), and all the samples derived from the corresponding Mock-treated plants were labeled with the alternative dye (i.e., Cy5). The dyes used for labeling RNA from a given treatment type (Dex and Mock) were switched for two of the replicate experiments, to reduce dye-related artifacts. Dex- and Mock-derived samples for each timepoint and biological replicate were co-hybridized. This experimental setup resulted in a total of 5 hybridizations per set (0h, 2h, 4, 8h, and 12h; Dex vs. Mock at each timepoint), and two biological replicate sets labeled with each dye polarity (Mock-Cy3/Dex-Cy5, and vice versa). The combined ratio data results are available as a supplementary file on the Series record.

2010-04-02 | E-GEOD-20182 | biostudies-arrayexpress

Meyerowitz Lab Arabidopsis Operon Array v4 - 4000B scanner - AP1-GR ap1cal inflorescences - time series (hours)

2010-04-02 | E-GEOD-20183 | biostudies-arrayexpress

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