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Omics score: 6

Transcription profiling by high throughput sequencing in different primary root segments of Zea mays

ABSTRACT: In this study RNA-sequencing was used to monitor gene expression changes in four tissues (meristematic zone, elongation zone, and cortex and stele of the mature zone) of maize (Zea mays L.) primary roots in response to water deficit to gain a better understanding of the mechanisms underlying drought tolerance.

REANALYSIS of: E-MTAB-4297

ORGANISM(S): Zea mays

PROVIDER: E-MTAB-4297 | ExpressionAtlas | 2016-02-02

REPOSITORIES: ExpressionAtlas

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Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.).

Tai Huanhuan H Lu Xin X Opitz Nina N Marcon Caroline C Paschold Anja A Lithio Andrew A Nettleton Dan D Hochholdinger Frank F

Journal of experimental botany 20151130 4

Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of prima ...[more]

PMID: 26628518

Similar Datasets

Transcription profiling by high throughput sequencing in different primary root segments of Zea mays

Project description:In this study RNA-sequencing was used to monitor gene expression changes in four tissues (meristematic zone, elongation zone, and cortex and stele of the mature zone) of maize (Zea mays L.) primary roots in response to water deficit to gain a better understanding of the mechanisms underlying drought tolerance.

2015-10-08 | E-MTAB-4297 | ArrayExpress

Transcription profiling by high throughput sequencing of maize (B73) shoot-borne root stele response to local high nitrate stimulation

Project description:In this study RNA-sequencing was used to monitor gene expression changes in stele tissue of maize (Zea mays L.) shoot-borne roots in response to local high nitrate stimulation to gain a better understanding of the mechanisms underlying nitrate signal and lateral root development.M

2016-02-02 | E-MTAB-4253 | ExpressionAtlas

Transcription profiling by high throughput sequencing of maize (B73) shoot-borne root stele response to local high nitrate stimulation

2015-10-08 | E-MTAB-4253 | ArrayExpress

Transcription profiling by high throughput sequencing of young maize primary roots in response to low water potentials

Project description:In this study a transcriptomic approach (RNA-sequencing) was utilized to elucidate molecular responses of maize (Zea mays L.) primary roots of the inbred line B73 to water deficit to gain a better understanding of the mechanisms underlying drought tolerance. Kernels of the maize inbred line B73 were germinated in paper rolls soaked with distilled water until seedlings had a primary root length of 2 to 4 cm. For mild and severe water deficit conditions, seedlings were transferred to PEG8000 solution with water potentials of -0.2 MPa and -0.8 MPa, respectively. Water deficit treatment was applied for 6 h and 24 h. Each treatment was performed in four biological replicates each consisting of 10 roots.

2016-04-28 | E-MTAB-4325 | ExpressionAtlas

Transcription profiling by high throughput sequencing in different developmental stages of Zea mays subsp. mays tissues

Project description:Zea mays subsp. mays Transcriptome or Gene expression Atlas.

2016-02-04 | E-MTAB-4342 | ExpressionAtlas

Transcription profiling by high throughput sequencing of young maize primary roots in response to low water potentials

2014-05-03 | E-MTAB-4325 | ArrayExpress

Comparative histone modification profiling revealed developmentally regulated acetylation on upstream promoters of C4 genes and potential C4 regulators

Project description:We analysed genome-wide histone H3 lysine 4 trimethylation and histone H3 lysine 9 acetylation, two modifications typically associated with active genes, in meristematic cells at the base and expanding cells in the maturing zone of the maize (Zea mays) leaf. These data were compared to transcript levels of associated genes. Our data revealed that for individual genes fold-changes in histone modification and transcript abundance were much better correlated than absolute intensities. When focusing on regulated modification sites, we identified secondary upstream H3 lysine 9 acetylation peaks (SUPs) on upstream promoter regions of approximately 6% of all acetylated genes. SUPs showed stronger regulation than the previously described acetylation peaks at transcription initiation sites, were more often found on genes that were upregulated towards the maturing zone than on downregulated genes, and were significantly enriched on photosynthetic genes. We identified SUPs on all genes encoding enzymes of the C4 cycle. Moreover, SUPs were enriched in four lists of candidate C4-associated genes that were derived from previous transcriptomic studies. Based on these data, we used highly regulated SUPs as an epigenetic mark to identify new genes potentially involved in C4 metabolism. This approach also allowed the identification of ethylene response elements as highly enriched cis-acting elements in SUP regions. Our data suggest co-evolution of epigenetic promoter elements during the establishment of C4 photosynthesis. Comparative analysis of H3K9ac, H3K4me3 and the transcription between two developmental zones within one maize leaf.

2015-09-03 | E-GEOD-67551 | ArrayExpress

Transcription profiling by high throughput sequencing in different developmental stages of Zea mays subsp. mays tissues

Project description:Zea mays subsp. mays Transcriptome or Gene expression Atlas.

2012-09-13 | E-MTAB-4342 | ArrayExpress

Transcription profiling by high throughput sequencing of maize embryo and endosperm during development

Project description:Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues.

2016-04-07 | E-MTAB-4395 | ExpressionAtlas

Transcription profiling by high throughput sequencing of maize inbred lines B73, Mo17 and Oh43 under control and stress conditions

Project description:Transcriptome of Zea mays genotypes under control and stress conditions. Stress conditions include heat, cold, salt, and UV. We extracted and sequenced RNA from 14 day old seedlings of inbred lines B73, Mo17 and Oh43 grown using standard conditions as well as seedlings that had been subjected to cold (5°C for 16 hours), heat (50°C for 4 hours), high salt (watered with 300 mM NaCl 20 hours prior to collection) or UV stress (2 hours). For each stress the plants were sampled immediately following the stress treatment and there were no apparent morphological changes in these plants relative to control plants.

2016-04-28 | E-MTAB-4258 | ExpressionAtlas

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