E-MTAB-4202
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-4202 | ExpressionAtlas | 2016-04-07
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-4202-analysis-methods.tsv | Tabular | |||
| E-MTAB-4202-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-4202-coexpressions.tsv.gz | Tabular | |||
| E-MTAB-4202-configuration.xml | Xml | |||
| E-MTAB-4202-factors.xml | Xml |
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Project description:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an inflorescence have not been described. In this study we analyzed gene expression during Arabidopsis thaliana meristem development from day 7 to 16 after germination in one-day increments. The dynamics of the expression of the main flowering regulators were consistent with previous reports: notably, the expression of FLOWERING LOCUS C (FLC) decreased over the course of the time series while expression of LEAFY (LFY) increased. This analysis revealed a developmental time point between 10 and 12 days after germination where FLC expression had decreased but LFY expression had not yet increased, which was characterized by a peak in the number of differentially expressed genes. GO enrichment analysis of these genes identified an overrepresentation of genes related to the cell cycle, suggesting that during transition to the flowering stage a change in dynamics of cell division takes place. In particular, we hypothesize that a subset of the meristematic cells experiences a forced exit from G0 at day 10. Finally, we observed an acceleration of the cell cycle at day 11, which may be linked to meristem reorganization preceding activation of LFY.
2015-07-21 | E-MTAB-4202 | biostudies-arrayexpress
Project description:We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.
2019-12-14 | GSE142030 | GEO
Project description:SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase. We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are directly bound by SVP by means of ChIP sequencing (Illumina Solexa Sequencing) approach during the two distinct phases of development. Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for chromatin extraction and subsequent immunoprecipitation using GFP antibody. The identification of genome wide binding sites of SVP using the ChIP-SEQ approach were performed in the vegetative phase using pSVP::SVP-GFP svp-41 and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and pSVP::SVP-GFP svp-41 inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.
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Project description:SVP is a key MADS-box transcription factor for Arabidopsis development since it acts both during vegetative and reproductive phases where it plays different roles probably by interacting with different partners to regulate specific sets of target genes. In fact, whereas SVP functions as a repressor of floral transition during the vegetative phase, it works as floral meristem gene during reproductive phase. We studied the behavior of SVP during two distinct developmental phases: the vegetative and reproductive phase. The aim of these studies is to identify subsets of genes that are regulated by SVP by means of Arabidopsis Tiling 1.0R Arrays (Affymetrix) during the two distinct phases of development. Arabidopsis thaliana seedlings and inflorescences were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. To evaluate the amount of SVP expression in the vegetative phase we used svp-41 single mutant and wild-type seedlings grown for 2 weeks in Short Day (SD) conditions (8 h light/16 h dark); for the reproductive phase we used wild-type and svp-41 agl24-2 ap1-12 triple mutant inflorescences grown for 2 weeks in SD conditions and then moved in (LD) conditions (16 h light/16 h dark). The inflorescences were collected at 2 weeks after bolting.
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Project description:We sequence mRNA of WT and pgp1 seedling grown at 16°C, day 8 after germination, ZT 16
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Project description:Enzymatic methyl-seq (EM-seq) was used to profile whole-genome cytosine methylation in Arabidopsis thaliana wild type and nuclear-envelope mutants that display premature aging phenotypes. All lines are in the Col-0 background and include wild-type Col-0, single mutants in crwn1, crwn2, crwn3, crwn4 and kaku4, the crwn1 crwn4 double mutant, and a second-generation kaku4 line (kaku4-G2). For late-age samples, rosette tissue was harvested from soil-grown plants under short-day conditions (8 h light / 16 h dark) at 150 days after sowing, when nuclear-envelope mutants show strong rosette senescence, meristem failure and reduced lifespan. For young reference samples, whole seedlings of Col-0 (wildtype) and kaku4-G2 were collected at 12 days after sowing. For each genotype and age, pooled material from multiple plants was used to obtain sufficient genomic DNA. Genomic DNA was extracted from each pooled sample and converted using the NEBNext Enzymatic Methyl-seq (EM-seq) protocol, followed by Illumina library preparation and paired-end high-throughput sequencing. This dataset is used to (i) quantify genome-wide CG, CHG and CHH methylation in wild type and nuclear-envelope mutants, (ii) compare age-dependent methylation drift between 12-day seedlings and 150-day short-day rosettes, and (iii) identify chromatin-state- and transposable-element-specific methylation changes associated with nuclear-envelope dysfunction and premature aging in Arabidopsis.
2026-07-22 | E-MTAB-16263 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage. Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis. Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development. Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives. Wild-type broccoli mRNA profiles of seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas were generated by deep sequencing, three biological replicates pooling together for each tissue, using Illumina Myseq platform.
2014-03-18 | E-GEOD-53298 | biostudies-arrayexpress
Project description:Purpose: The goals of this study are to analyze the transcriptome of five time point in broccoli seed germination and sprout development and to find the putative glucosinolate metabolism genes in the stage. Methods: Total mRNA of germinated seeds, 3 day cotyledons, 7 day botyledons, 11 day cotyledons and 11 day euphyllas of wild-type broccoli were harvested. Each sample was harvested in three independent biological replicates with equal weight and subsequently pooled together for sequencing. The sequence reads that passed quality filters were de novo assembled using VELVET followed by OASES. Then the assembled unigenes were used for the abundance and functional analysis. Results: A total of ~85million 251bp reads were obtained. After de novo assembly and searching the assembled transcripts against the Arabidopsis thaliana and Nr databases, 19,441 top-hit transcripts were clustered as unigenes with an average length of 2,133bp. These unigenes were classified according to their putative functional categories. Cluster analysis of total unigenes with similar expression patterns and differentially expressed unigenes among different tissues,as well as transcription factor analysis were performed. We identified 25 putative glucosinolate metabolismgenes sharing 62.04-89.72% nucleotide sequence identity with the Arabidopsis orthologs. This established a broccoli glucosinolate metabolic pathway with high colinearity to Arabidopsis. Many of the biosynthetic and degradation genes showed higher expression after germination than in seeds; especially the expression of the myrosinaseTGG2 was 20-130 times higher.These results along with the previous reports that glucosinolate concentration decreased exponentially once after germination indicate the breakdown products of glucosinolates may play important roles in broccoli seed germination and sprout development. Conclusion: Our study provides the largest genetic resource of broccoli to date. These data will pave the way for further studies and genetic engineering of broccoli sprouts to develop functional vegetables containing high levels of the anticarcinogenic glucosinolates. They will also provide new insight into the genomic research of this species and its relatives.
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