Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1097301 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR28579882_1.fastq.gz | Fastqsanger.gz | |||
| SRR28579882_2.fastq.gz | Fastqsanger.gz | |||
| SRR28579883_1.fastq.gz | Fastqsanger.gz | |||
| SRR28579883_2.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq of tobacco explants cultured by different NAA concentrations during in vitro tissue culture provides high-resolution transcriptome data,which provides a novel direction and theoretical basis for improving gene editing efficiency in plants by modulating chromatin accessibility through auxin signaling and tissue culture conditions.
2024-12-01 | GSE280743 | GEO
Project description:RNA-seq of tobacco explants cultured by different NAA concentrations during in vitro tissue culture
| PRJNA1180453 | ENA
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation.
2022-11-21 | E-NASC-15 | biostudies-arrayexpress
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Experiment Overall Design: 6 samples
2008-06-14 | E-GEOD-6148 | biostudies-arrayexpress
Project description:The formation of vascular tissue occurs when cellulose, hemicellulose, lignin and other wall components are deposited within the primary cell wall. These secondary thickened cells then undergo programmed cell death producing a network of empty cells with which water and ions can be transported throughout the plant. The hormones auxin and cytokinin are the principle signals for vascular tissue initiation. As a consequence cells cultured in-vitro can be converted into vascular tissue with the addition of exogenous auxin and cytokinin. We have created an in-vitro cell system, using callus produced from leaves that can be induced to form vascular tissue. Leaves are callused on induction media for two weeks. The callus is then transferred to liquid media and incubated under optimum conditions resulting in an increase in vascular tissue formation. Approximately 20% of cells will differentiate during the incubation period. The alteration of cytokinin concentration affects the ability of the cultured cells to undergo differentiation. Consequently callus incubated in liquid media, containing lower cytokinin concentrations, will undertake relatively little differentiation. Samples have been isolated from cell cultures at different time points and different hormone concentrations during incubation. Quantitative PCR using the marker AtCesA7, which encodes a cellulose synthase subunit specific to secondary wall deposition, was used as a guide to determine periods of high and low vascular differentiation. This system provides an opportunity to compare gene expression between differentiating and non differentiating cells and allow the identification of genes up regulated during vascular tissue formation. Keywords: time_series_design; compound_treatment_design
2007-01-22 | GSE6148 | GEO
Project description:Leaf explants of the superembryogenic Medicago truncatula line 2HA were treated with auxin (1-naphthaleneacetic acid) for one week to induce the formation of roots (Imin et al J Exp Bot 58:439-451). Gene expression in the leaves and the NAA treated tissue cultures was compared to identify transcripts expressed during the commitment to root formation in tissue culture. We have used the Affymetrix Medicago Genome Array GeneChip to compared gene expression in Medicago truncatula leaves and leaf explants that have been cultured for one week on NAA, to identify genes expressed during the commitment to root formation in tissue culture. Keywords: Cell type comparison
2007-10-01 | GSE8138 | GEO
Project description:Leaf explants of the superembryogenic Medicago truncatula line 2HA were treated with auxin (1-naphthaleneacetic acid) for one week to induce the formation of roots (Imin et al J Exp Bot 58:439-451). Gene expression in the leaves and the NAA treated tissue cultures was compared to identify transcripts expressed during the commitment to root formation in tissue culture. We have used the Affymetrix Medicago Genome Array GeneChip to compared gene expression in Medicago truncatula leaves and leaf explants that have been cultured for one week on NAA, to identify genes expressed during the commitment to root formation in tissue culture. Experiment Overall Design: Medicago truncatula 2HA leaves and leaf explants treated with NAA for one week were collected; total RNA was extracted and used for hybridization to Affymetrix arrays
2008-06-17 | E-GEOD-8138 | biostudies-arrayexpress
Project description:The in vitro cell culturing witnessed its applications in both scientific research and industrial activities, its optimization leads to practical benefits, either through shortening the doubling time, or simplification of engineering requests, or both. Literature searching highlighted a role of a synthetic auxin derivative 1-Naphthaleneacetic acid (NAA) in optimizing plant cell culturing. Here, by measuring cell counts and their activities via CCK8 tests, we observed an up to 2-fold increase in the yield of in vitro cultured human cells. We tested different types of human cell lines and primary natural killer cells, found that NAA was effective in all the cells tested. The PI staining and FACS analysis suggested that NAA did not affect the cell cycling. Apoptosis-specific dye staining analysis implicated that NAA rescued cell death. We further did bulk RNA sequencing and identified the lipid metabolism-engaging and anti-apoptosis gene, ANGPTL4, was enhanced in expression upon NAA treatment. Studies on ANGPTL4 knockout cells indicated that ANGPTL4 is required for NAA-mediated response. Thus, our data identified a beneficial role of NAA in human cell culturing and highlighted its potency in the in vitro cell culturing
2023-10-18 | GSE245281 | GEO
Project description:Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome.
2017-06-01 | GSE82138 | GEO
Project description:We optimised an in vitro culture model for mouse oocytes starting from immature oocytes to get mature oocytes and investigated the effect of oxygen concentrations on the cultured oocytes (5 % vs 20% oxygen). The cultured oocytes were size-selected in both conditions. We generated expression and methylation profiling (RNA-Seq, RRBS, PBAT) by high throughput sequencing from these size selected oocytes and compared the results with in vivo size oocytes. Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex-vivo culture condition.
2021-07-08 | GSE164864 | GEO