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Expression data from Arabidopsis mature siliques

ABSTRACT: Analysis of the transcriptomes of nearly ripe siliques (18-19 DAP) of the rdo2-1, rdo3 and hub1-2 (rdo4) mutants in comparison with wild-type Ler, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array. The experiment includes rdo2, rdo3, and rdo4 as well the Ler genotypes with three biological replicates for each. Therefore in total there are 12 arrays

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Annaick Carles

PROVIDER: E-GEOD-28446 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy.

Liu Yongxiu Y Geyer Regina R van Zanten Martijn M Carles Annaick A Li Yong Y Hörold Anja A van Nocker Steven S Soppe Wim J J WJ

PloS one 20110725 7

The life of a plant is characterized by major phase transitions. This includes the agriculturally important transitions from seed to seedling (germination) and from vegetative to generative growth (flowering induction). In many plant species, including Arabidopsis thaliana, freshly harvested seeds are dormant and incapable of germinating. Germination can occur after the release of dormancy and the occurrence of favourable environmental conditions. Although the hormonal control of seed dormancy i ...[more]

PMID: 21799800

Similar Datasets

Expression data from Arabidopsis mature siliques

Project description:Analysis of the transcriptomes of nearly ripe siliques (18-19 DAP) of the rdo2-1, rdo3 and hub1-2 (rdo4) mutants in comparison with wild-type Ler, using Affymetrix GeneChip Arabidopsis ATH1 Genome Array.

2011-04-08 | GSE28446 | GEO

Small RNAs in Arabidopsis hybrid siliques

Project description:Five days post-fertilization siliques were collected for RNA extraction. After purification, small RNA libraries were generated for high throughput sequencing. Resulting sequences were analyzed to determine the contribution of the paternal genome to the small RNA transcriptome. Keywords: Epigenetics 4 unique samples. small RNAs purified from Arabidopsis siliques 5 days after pollination. Samples were selfed or hybrid crosses between ecotypes Columbia (Col) and Landsberg erecta (Ler).

2009-03-24 | E-GEOD-15348 | biostudies-arrayexpress

RNA-seq of Arabidopsis thaliana Col-0 siliques

Project description:Paired-end Illumina RNA sequencing of Arabidopsis thaliana Col-0 siliques.

2016-11-16 | GSE89617 | GEO

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

Small RNAs in Arabidopsis hybrid siliques

2009-03-24 | GSE15348 | GEO

Salt stress downregulates 2-hydroxybutyrylation in Arabidopsis siliques

Project description:In this study, we compared the siliques from Arabidopsis thaliana under salt stress (Ss) with those in the control (Cs). The results showed that Khib was abundant in siliques. However, there were certain significant differences between the Ss and the Cs: Totally 3,810 normalized Khib sites on 1,254 proteins were identified in siliques under salt stress, and Khib was up-regulated at 96 sites on 78 proteins while down-regulated at 282 sites on 205 proteins in Ss silique. Among them, 13 proteins, including F4IVN6, Q9M1P5, and Q9LF33, had sites with the most significant regulation Khib modification. Bioinformatics analysis suggests that Khib mainly participates in glycolysis/gluconeogenesis and endocytosis. In particular, there were 117 Khib-modified proteins that were mapped to the protein interaction database, and the proteins with the most significant up-regulation of Khib sites were on P46422, O82514, Q38970, Q9LD57, and Q9STW6, while the most down-regulated sites were on Q9M9K1, Q9SF16, O24456, P83484, Q9FWA3, and P54609. In the KEGG pathway enrichment analysis, Khib-modified proteins were enriched in several pathways related to energy metabolism, including gluconeogenesis pathway, pentose phosphate pathway, and pyruvate metabolism.

2021-12-30 | PXD028116 | Pride

Transcriptome profiling of siliques at 4 developmental stages in Arabidopsis

Project description:To search for the differential expressed genes during post-fertilization and embryonic development in Arabidopsis, We profiled transcriptome of siliques at 4 developmental stages using RNA-seq based on poly(A) selection. Each RNA library yielded 100 million 101-bp paired-end reads.Using Tophat and Cufflinks with the Arabidopsis TAIR10 annotation as reference, we identified 33,451 assembled transcripts in 4 samples. Of them, 5,608 were up-regulated genes in at least one sample. A group of them are preferentially expressed at mature green-stage of seeds. Transcriptome profiling in 0-5 day, 6-10 day, 11-15 day and 16-20 day post-anthesis siliques

2016-03-28 | E-GEOD-55866 | biostudies-arrayexpress

Transcriptome-wide RNA 5-methylcytosine methylation in siliques of Arabidopsis thaliana

Project description:Here we use bisulfite conversion of rRNA depleted RNA combined with high-throughput Illumina sequencing (RBS-seq) to identify single-nucleotide resolution of m5C sites transcriptome-wide in Arabidopsis thaliana siliques. m5C sites were also analyzed in an Arabidopsis T-DNA knockout for the RNA methyltransferase TRM4B.

2017-04-07 | GSE80050 | GEO

Transcriptome analysis of Arabidopsis siliques

Project description:Transcriptome analysis of Arabidopsis siliques reveals genes with essential roles in fruit development and maturation

| PRJEB25745 | ENA

RNA-seq of Arabidopsis thaliana siliques from WT and MYB73 overexpression lines

Project description:This experiment seeks to elucidate the functional role of MYB73 in Arabidopsis thaliana siliques via differential gene expression (DGE) analysis. Total RNA were extracted from pooled Arabidopsis siliques at 12 days after flowering (DAF) for 3 biological replicates from WT and MYB73-OE lines. RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) for Illumina according to the manufacturer’s instruction and sequenced with Novaseq-6000 (Illumina) using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.

2024-11-01 | E-MTAB-14541 | biostudies-arrayexpress

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