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Barely leaf dark-induced senescence

ABSTRACT: Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments. Time-course experiment, two-color, common reference design. All of the data were obtained from material collected in three independent, time-separated leaf senescing experiments (biological replicates). In each replicate, samples from senescing leaves (3 Days, 7 Days, 10 Days) were compared to samples collected before the senescence induction (Day 0). 3 biological replicates.Cy5-labeled samples of interest (Day 0, Day 3, Day 7 and Day 10 from each biological replicate) were each hybridized against a Cy3-labeled common reference (RNA pool of all samples) on a total of 12 microarrays.

ORGANISM(S): Hordeum vulgare

SUBMITTER: Agnieszka Zmienko

PROVIDER: E-GEOD-62539 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Barley leaf dark-induced senescence

Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments.

2014-10-22 | GSE62539 | GEO

Analysis of isolated Plastoglobules from Arabidopsis thaliana WT and M48 null mutants.

Project description:We studied the function of PG localized protease, PGM48 both in vitro and in vivo during natural senescence in Arabidopsis thaliana.Our results show that PGM48 is a metalloprotease and a senescence inducible protein. In vitro assay by recombinant protein revealed a proteolytic activity. Quantitative proteome analysis of PGs from senescing rosettes of overexpression plants lines showed a significantly reduced level of CAROTENOID CLEAVAGE ENZYME 4 ( CCD4) protein but 2-3 fold higher level of phytyl-esterase (PES1) compared to wild type; the opposite results were found in RNAi lines. Yeast-2-hybrid analysis and in vitro pull-down experiments showed that PGM48 interacts with the kinase ABC1K3, PES1 and CCD4, but not with chlorophyll catabolic enzymes. We propose that PGM48 acts as a positive regulator of leaf senescence.

2019-04-09 | PXD003684 | Pride

Dark-induced senescence time course of ANAC017 mutant lines in Arabidopsis

Project description:The role of ANAC017 in leaf senescence was assessed by covering leaf 6-7 of 5 week old plants. Samples of Col-0, anac017 knock-out and two ANAC017 overexpression lines were compared of day 0, 1 and 3 of the timecourse. ANAC017 OE lines show accelerated senescence during this time.

2021-05-06 | E-MTAB-8478 | biostudies-arrayexpress

Transcription profiling of Arabidopsis leaf senescence

Project description:1. Comparison of two near isogenic lines between which the genome differs only for the region of the leaf-yellowing QTL Y3-4 on chromosome III. Experiment description: The lines HIF404-Sha and HIF404-Bay were grown on 3 mM nitrate in growth chamber according to Loudet et al . (2002, TAG 104:1173-84) until phenotypic yellowing symptoms differed between them. Plants were collected 49 days after sowing. 2. Comparison of sugar effect on the leaf senescence progress using three RIL from the Bay-0 x shahdara population that exhibited differential leaf yellowing symptoms. Experiment description: The recombinant inbred lines RIL310 (hypersenescing and early-senescing), RIL232 (early--senescing) et RIL045 (late-senescing) were grown in petri dishes (4,7 mM Nitrogen, with (LNG) or without (LN) glucose 2% until some difference of Fv/Fm trait can be observed (Wingler et al. 2004, New Phytol, 161 : 781-789). Growth experiments were performed in A. Wingler lab, University College of London.

2006-04-01 | E-MEXP-387 | biostudies-arrayexpress

Integrated transcriptomics and miRNAomics provide insights into the regulatory networks associated with coleoptile senescence in rice

Project description:Purpose: To understand the transcriptional changes during coleoptile senescence, transcriptome libraries were constructed from control and senescence tissues and subjected to Illumina sequencing. Methods: Rice seeds were surface sterilized and submerged for seven days in sterile water. The seeds with coleoptile was transferred to aerobic condition. Senescence progression was monitored and tissues of un-senesced and senesced coleoptiles were harvested. Total RNA was isolated from the harvested tissues. mRNA libraries were generated and sequenced as 101 bp paired-end reads by using Illumina Hiseq 4000. Results: Our analysis revealed that 3166 transcripts were differentially expressed in senescing coleoptile (Day 2) samples as compared to the control. Furthermore, 44 and 273 transcripts showed specific expression in control and day 2 samples, respectively. From the functional category analysis, we observed that 197, 182, 99 and 88 transcripts belonging to signalling, transcription factors, hormone signalling and transporters respectively were differentially expressed during coleoptile senescence . And 15, 12, 3, and 6 transcripts showed senescence specific expression patterns in the transporters, transcription factors, signalling and hormone signalling categories respectively. Conclusions: The present study has generated a comprehensive resource of the molecular networks that enrich our understanding of the fundamental pathways regulating coleoptile senescence in rice.

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Gene expression analysis of untreated and NT-shRNA transduced kidney proximal tubular epithelial cells (PTECs) at day 6 and day 16 after transduction, as well as SETD2-shRNA transduced PTECs at day 25 after transduction.

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2016-01-09 | E-GEOD-72792 | biostudies-arrayexpress

A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves (Dark Induced Senescence).

Project description:A network model has been generated that describes the immediate gene expression cascade surrounding three similar but distinct NAC transcription factors that have roles to play in leaf senescence and in many stress responses in Arabidopsis. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1 hybrid analysis and modeling using gene expression time course data has been used to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modeling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions.. Gene expression measurements in mutants of ANAC019 and ANAC055 at different times during leaf senescence have shown a distinctly different role for each of these genes. To assess mutant response to Dark Induced Senescence (DIS), leaf5 from transplanted rosettes, subjected to dark conditions, from Col-0, myb2 (genotype IM24) and myb108 (genotype BOS1) knockout plants, were photographically assessed for red/green ratio. When the average ratio for Col-0 samples was >0.8, leaf 5 for Col-0, myb2 and myb108 lines was harvested (4 biological replicates). The same sampling procedure was then performed on consecutive days to sample as senescence progressed. Analysis of expression differences between Col-0 and myb2 and Col-0 and myb108 under each condition, using dye swaps, was performed using the R Bioconductor package limmaGUI (Wettenhall and Smyth, 2004).

2013-04-23 | E-GEOD-45595 | biostudies-arrayexpress

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2021-11-24 | PXD029200 | Pride

Spatial Coupling of mTOR and Autophagy Augments Secretory Phenotypes

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2011-05-04 | E-GEOD-28464 | biostudies-arrayexpress

Microarray analysis to detect whether the genome-wide gene expression profile of fibroblast-induced neurons resembles primary neurons

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