OBP4 modifies root growth, cell elongation and callus formation
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE80486 | GEO | 2016/10/06
SECONDARY ACCESSION(S): PRJNA319041
REPOSITORIES: GEO
Similar Datasets
Project description:Arabidopsis thaliana plant expressing 35S:WIND1 shows callus-like morphology without hormone treatment. Transcriptomes of the callus-like cell expressing 35S:WIND1, callus of T87 cultured cell, 2,4-D-induced callus and control seedling plant were compared by Agilent microarray.
2011-05-18 | GSE21631 | GEO
Project description:Arabidopsis thaliana plant expressing 35S:WIND1 shows callus-like morphology without hormone treatment. Transcriptomes of the callus-like cell expressing 35S:WIND1, callus of T87 cultured cell, 2,4-D-induced callus and control seedling plant were compared by Agilent microarray. Comparison of four kinds of Arabidopsis thaliana plants. Biological replicates: three for each.
2011-05-17 | E-GEOD-21631 | biostudies-arrayexpress
Project description:Regeneration is common in plants and transcription factors greatly contribute to this versatility of flowering plants; however, the evolution of this capability has hardly been explored. The callus can be induced from an intact plant rather than an explant in the water fern Ceratopteris richardii and the employed media are very different. The callus was verified having resulted in indirect de novo shoot organogenesis (IDNSO). Hundreds of genes were differentially expressed between the proliferating and the differentiating callus, hinting at significant changes in photosynthesis and hormone response. Many transcription factors were also differentially expressed, providing cues on how the callus proliferated and differentiated. STM-, ANT-, and ESE3-like transcription factor were simultaneously expressed in the vascular-initial-like cells in the callus, thus identifying a key tissue in callus differentiation; furthermore, they might have undergone subfunctionalization or neofunctionalization during evolution. Therefore, IDNSO was considered both conserved and diversified throughout vascular plants.
2022-09-09 | GSE212819 | GEO
Project description:Profiling the transcriptome of the early stage of Arabidopsis callus induction variable_1 = root explants variable_2 = aerial organ explants variable_3 = 0 h on callus inducing medium variable_4 = 12 h on callus inducing medium variable_5 = 24 h on callus inducing medium variable_6 = 48 h on callus inducing medium variable_7 = 96 h on callus inducing medium
2012-07-22 | E-GEOD-29543 | biostudies-arrayexpress
Project description:The applications of plant callus regeneration has been widely spreaded in agricultural improvement. By using immature sorghum embryos as explants, progress in successful genetic transformation has been made in sorghum. However, the underlying mechanism of callus differentiation is still largely unknown in sorghum. Here, we described three types of callus with different abilities of redifferentiation (Callus I-III), undergoing distinct induction from immature embryo in the variety of Hiro-1. In comparison to the non-embryonic Callus III who lost the ability of regeneration, the Callus I produced only some characterized adventitious roots and the embryonic Callus II is sufficient to regenerate whole plants. Genome-wide transcriptome profiles were performed to reveal the underlying mechenisms. The numbers of differentially expressed genes for the three types of callus vary from 5906 to 8029. Principal component analysis analysis demonstrated that gene expression patterns of Callus I and II were totally different from that of Callus III and differential leaves from Callus II, indicating that the compassions of Callus I and II provide clues for revealing regulations of regeneration in sorghum callus. Notably, KEGG and GO analysis showed that plant ribosome, lignin metabolic process, and metabolism of starch and sucrose are main processes that are associated with callus differentiation. Taken together, the results contributed the elucidation of molecular regulation in three types of callus with several regeneration abilities in sorghum.
2019-12-31 | GSE140958 | GEO
Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation. Comparison of young and mature Arabidopsis hypocotyls either with or without auxin treatment for 1 day
2011-06-19 | E-GEOD-27508 | biostudies-arrayexpress
Project description:Transcriptional profiling of age-related change of callus formation capability in Arabidopsis hypocotyls Organogenesis in vitro consists of many aspects such as phytohormone perception, dedifferentiation of differentiated cell to acquire organogenic competence, and re-entry of quiescent cells into cell cycle. In this study, we established an in vitro experimental system to study the age-dependent callus formation capacity in Arabidopsis. Interestingly, mature (35- to 38-day-old) hypocotyl explants exhibited better callus-forming potential than that of juvenile (7- to 10-day-old), determined by callus growth rates. To explore genome-wide expression changes underlying the phenomenon of age-dependent callus formation, a transcriptome-based analysis was performed. Gene expression profiling indicated that age-dependent callus formation capacity was associated with changes in phytohormone (auxins, cytokinins, abscisic acid, brassinosteroids and gibberellins) homeostasis, epigenetic mechanism and the cell cycle regulation. Besides, we identified two groups of genes involved in age-dependent callus formation capacity: (1) positive regulatory and (2) negative regulatory categories, i.e. genes that were significantly up- or down-regulated during callus formation derived from mature explants, respectively. One gene encoding DNA-binding protein (VARIANT IN METHYLATION 1, VIM1) belonging to the positive regulatory category was selected for functional analysis and assessment of age-dependent callus formation capacity. Indeed, vim1 reduced the efficiency of callus formation in mature explants, but not in juvenile. The result suggests that VIM1 plays an important role in regulating age-dependent callus formation capacity. Taken together, the investigation will help to better understand the molecular regulatory mechanism of age-dependent callus formation.
2011-06-19 | GSE27508 | GEO
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE156991 | GEO
Project description:Skeletal stem/progenitor cells are critical for fracture repair by providing osteochondro precursors in the callus, which is impaired in aging. However, the molecular signatures of callus skeletan progenitor cells during aging is not known. We performed single-cell RNA sequencing on CD45-CD31-Ter119- skeletan progenitor cells isolated from young and aged mouse calluses.
2022-04-01 | GSE199755 | GEO