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Transcriptome analysis of Arabidopsis dry seeds

ABSTRACT: Transcriptome analysis of Arabidopsis dry seeds

PROVIDER: PRJNA741902 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14929805.fastq.gz	Fastqsanger.gz
	SRR14929806.fastq.gz	Fastqsanger.gz
	SRR14929808.fastq.gz	Fastqsanger.gz
	SRR14929809.fastq.gz	Fastqsanger.gz
	SRR14929811.fastq.gz	Fastqsanger.gz

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Transcriptome analysis of Arabidopsis dry seeds

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transcriptome and translatome of arabidopsis wt seeds according to dormancy-transcriptomic and translatomic analysis of Arabidopsis seeds

Project description:au13-12_polysome - transcriptome and translatome of arabidopsis wt seeds according to dormancy - Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA. - At harvest seeds are dormant. They stay dormant if they are stored at -20°C (D) and become non-dormant (ND) if they are stored 3 weeks at +20°C. Arabidopsis dormant seeds do not germinate at 25°C in darkness while non-dormant seeds do. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h or 24h at 25°C in darkness (3 biological replicates). Transcriptome and translatome are compared for Dormant vs Non-Dormant for 16h and 24 imbibition. In silico comparison will allow to compare transcriptome and translatome for each point and type of seeds and to compare the time points (16 vs 24h) for each type of sample.

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Comparison of histone deacetylase 9-1 mutant (SALK_001723) dry seed transcriptome with Col wild-type

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transcriptome and translatome of arabidopsis wt seeds according to dormancy-transcriptomic and translatomic analysis of Arabidopsis seeds

Project description:au13-12_polysome - transcriptome and translatome of arabidopsis wt seeds according to dormancy - Identification of transcripts that are differentially abundant (transcriptome) and transcripts that are addressed to translation (translatome) in imbibed Arabidopsis seeds in relation with dormancy. During imbibition of seeds (16h and 24h in darkness at 25Â°C, dormant and non-dormant seeds), transcriptome analysis is done on total RNA and translatome analysis on polysomal RNA. - At harvest seeds are dormant. They stay dormant if they are stored at -20Â°C (D) and become non-dormant (ND) if they are stored 3 weeks at +20Â°C. Arabidopsis dormant seeds do not germinate at 25Â°C in darkness while non-dormant seeds do. Total RNA and polysomal RNA (polysomal fractions purified on sucrose gradients) were extracted from imbibed seeds for 16h or 24h at 25Â°C in darkness (3 biological replicates). Transcriptome and translatome are compared for Dormant vs Non-Dormant for 16h and 24 imbibition. In silico comparison will allow to compare transcriptome and translatome for each point and type of seeds and to compare the time points (16 vs 24h) for each type of sample. 12 dye-swap - time course

2014-09-27 | E-GEOD-61809 | biostudies-arrayexpress

RNA-Seq on mpk8 and tcp14 mutants on dry and imbibited seeds - Dormancy release by phosphorylation

Project description:ngs2016_10_dormancy - RNA-Seq on mpk8 and tcp14 mutants on dry and imbibited seeds-Comparison of the expression of genes in wild seeds and in mpk8 and tcp14 mutants on dry seeds and at a precise imbibition time (24h, 25°C) and in the dark.-Dry harversted seed: WT, mpk8, tcp14, 24h of imbibition in dark at 25°C: WT, mpk8, tcp14.

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Comparison of histone deacetylase 9-1 mutant (SALK_001723) dry seed transcriptome with Col wild-type

Project description:Analysis of the transcriptome of dry hda9-1 mutant seeds with those of Col wild-type seeds, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array. The hda9-1 mutant has reduced primary seed dormancy. We used microarrays to dissect which genes are differentially expressed in the hda9-1 mutant to study the mechanisms how HDA9 affects seed dormancy and germination RNA was extracted from tagged dry 18-19-DAP siliques of wild-type Col and the hda9-1 mutant following an adapted protocol of the RNAqueous small scale Phenol-free total RNA isolation kit in addition with RNA isolation aid (Ambion, Austing, TX, USA), as described in Liu et al. (2011) PLoS ONE and Van Zanten et al. (2011) PNAS. Affymetrix GeneChip Arabidopsis ATH1 Genome-Micro hybridization was performed at the Max Planck Genome Centre Cologne. Three independent hybridizations of independent biological replicates, obtained from several dry siliques of at least five plants per replica, were performed.

2014-09-21 | E-GEOD-50786 | biostudies-arrayexpress

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Project description:We identified a regulator of Arabidopsis thaliana seed germination: FLOE1 (AT4G28300). We used RNA-seq to uncover genes that are diffenrentially regulated in dry seeds, imbibed seeds and seeds imbibed in 220mM NaCl.

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Proteomics Analysis of the UMK2 Mutation in Arabidopsis thaliana seeds

Project description:We compared the proteome of dry as well as germinating seeds of Arabidopsis thaliana wild type Col-0 with the respective proteomes from an umk2 (AT4G25280) frameshift mutant. Germinating seeds were incubated for 48 hours in 1/2-MS medium in Petri dishes at 4 degree Celsius followed by 24 hours of a phytochamber under long-day conditions. Protein extraction, digestion by SP3 workflow, and LC-IMS-MS/MS analysis as described in https://doi.org/10.1038/s41477-022-01308-6.

2023-07-03 | MSV000092331 | MassIVE

Gene expression in dormant, germinating and thermoinhibited Arabidopsis seeds

Project description:To establish the basis for understanding molecular mechanism of seed germination response to temperature, we analyzed transcriptomes in freshly harvested dormant and dry stored after-ripened seeds. The after-ripened seeds started to show visible germination from 36h after the start of imbibition, and almost all the seeds germinated after 3 days. The freshly harvested seeds stayed dormant by imbibition at 26°C, and germination of the after-ripened seeds was almost completely inhibited at 34°C. Total RNA was prepared from 0 (dry), 6 and 24h imbibed seeds to find regulatory genes of seed dormancy and germination.

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2019-11-12 | PXD013784 | Pride

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