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Dual response of wheat roots to ABA and nitrate [dataset2]

ABSTRACT: For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO3, and/or ABA for 3 hours. The roots of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).

ORGANISM(S): Triticum aestivum

PROVIDER: GSE302352 | GEO | 2026/07/11

REPOSITORIES: GEO

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Dual response of wheat roots to ABA and nitrate [dataset1]

Project description:For analysis of ABA and nitrogen treated transcriptome, wild-type wheat JW1 at 3 days after germination was removed endosperm and cultured on wheat nutrient culture medium containing 2 mM nitrate for 3 days, and then transferred to a nitrogen-free wheat nutrient culture medium for an additional 2 days. Following this, the wheat seedlings were exposed to wheat nutrient culture medium containing 2 mM KCl or 2 mM KNO3, and/or ABA for 3 hours. The roots of wheat were collected and subjected to total RNA extraction using the TriZol RNA extraction kit (TransGen Biotech).

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2019-01-20 | E-MTAB-7587 | biostudies-arrayexpress

The effect of nitrogen on wheat during drought and recovery after rehydration.

Project description:For transcriptomic analysis under drought, re-watering (RW), and re-watering with nitrate (RWN) conditions, wheat seedlings were germinated and transplanted into soil tanks once the first leaf emerged from the coleoptile, then irrigated with 2 L of wheat growth medium containing 5 mM nitrate, after which no further water was added. When soil moisture fell below 5%, seedlings were subjected to drought for one day before being re-watered with 2 L of medium containing either 0 mM (RW) or 5 mM (RWN) nitrate per tank. Leaf samples were collected from wheat seedlings during well-watered, drought, and at 3 hours, 1 day, and 5 days post-RW/RWN, and RNA was extracted for subsequent RNA-Seq analysis.

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Aspergillus niger exposed to combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH

Project description:Microarray analysis of Aspergillus niger under conditions with differing combinations of carbon source, nitrogen source, nitrogen concentration, and culture pH Fermentor cultures were grown in minimal medium (MM) at a constant temperature of 30 ± 0.5 ºC and with differing combinations of carbon source (either 277.5 mM glucose or 333.0 mM xylose), nitrogen source (NH4Cl or NaNO3) and nitrogen concentration (4x: 282.4 mM; 8x: 564.8 mM), and pH (pH4 or pH5) of the medium (M. Braaksma, A.K. Smilde, M.J. van der Werf, P.J. Punt, submitted for publication). At different time points samples were collected, quenched immediately in methanol at -45 ºC and centrifuged at -20 ºC to remove supernatant. Part of the biomass was frozen into liquid nitrogen and stored at -80 ºC for microarray analysis. For each of the 16 culture conditions one sample was selected for microarray analysis; samples were collected either around the time point carbon source depleted or a considerable time (~24 h) after carbon souce depletion. In addition some technical duplicates were included.

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Project description:rs05-06_dgpp - dgpp - The specific plant phosphorylated form of phosphatidic acid (PA), diacyglycerol pyrophosphate (DGPP) was recently shown to be a second messenger in abscisic acid (ABA) signaling. The aim of the project is to identify among the set of ABA-regulated genes the ones also regulated by DGPP and/or PA. - Five ml of 3 days-old suspension cells was incubated with ABA or lipids for 3 h under the conditions of culture. Lipids were emulsified by sonication for 1 mi, four times, at 4°C, in one ml of culture medium then added to 4 ml suspension cells. Cells were filtrated under vacuum, frozen in liquid nitrogen and RNA extracted. Dioleoyl PA and dioctanoyl PA are from Sigma, dioleoyl DGPP and dioctanoyl DGPP are from Avanti Polar Lipids. Keywords: treated vs untreated comparison

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Rice gene expression analysis

Project description:Four-day-old seedlings germinated in wet paper were transferred to solution culture with 0.1 mM Fe(III)-EDTA for five days. Then seedlings were transferred to solution culture without Fe or with 0.1 mM Fe(III)-EDTA for five days. Roots and shoots were separated and used for RNA extraction.

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RNA-seq in the basal nodes of nitrogen- and phosphorus-stressed Triticum aestivum var Cadenza (wheat) plants.

Project description:The aim of this study was to examine the transcriptional changes that govern low nitrogen (N) and low phosphorus (P) responses in basal nodes and may be associated with tiller suppression under nutrient-limiting conditions. For this purpose, RNA-seq was conducted in 18 days-old hydroponically grown wheat plants 8 days after the introduction of the plants to the nutrient limitation. The three different treatments were: Control (10 mM N, 1 mM P), Low N (0.1 mM N, 1 mM P) and Low P (10 mM N, 0.01 mM P). In total, four biological replicates were included per treatment. RNA-seq was conducted in total RNA extracted from 6 basal node samples pooled together per biological replicate. In this study, the basal node is defined as the 0.5 cm of the main shoot base, which includes the apical meristem, lateral buds, leaf meristems etc.

2023-01-17 | E-MTAB-11986 | biostudies-arrayexpress

Deciphering microRNAs and other small RNAs during the transition of dormant embryo into germinated embryo in larch (Larix leptolepis)

Project description:To investigate the roles of sRNAs in keeping embryo dormancy or germination in Larix leptolepis, we deciphered the endogenous "sRNAome" in dormant and germinated embryos. High-throughput sequencing of the sRNA libraries showed that dormant embryos exhibited a length bias towards 24-nt, while germinated embryos showed a bias towards a 21-nt and/or 22-nt length. Both of proportions for miRNAs to the non-redundant and redundant sRNAs were higher in germinated embryos than those in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. The proportion of 21-nt and 22-nt sRNAs increased in germinated embryos, which might attribute to the higher expression level of miRNAs. We identified a total of 160 conserved miRNAs from 39 families, 16 novel miRNAs, and 14 plausible miRNA candidates, of which novel and non-conserved known miRNAs might be the main contributors. These findings indicate that larch and possibly other gymnosperms have complex mechanisms of gene regulation involving sRNAs and miRNAs operating transcriptionally and post-transcriptionally during embryo dormancy and germination. One embryogenic cell line of Japanese larch (Larix leptolepis), designated as D878, with a high embryo maturation capacity was used in this study. Embryogenic callus were induced from immature embryos of larch on induction medium, followed by sub-culture, and culture on ABA-containing mature medium in a dark environment at 25 2 C. After cultured 45 days in mature medium, embryogenic calli developed into mature somatic embryos. In our study, the samples were harvested at day 57, one sample was collected after mature embryos continued to stay for 12 days on ABA-containing medium, and the other one was harvested after cultured for 12 days on ABA-removing medium. All samples were snap-frozen in liquid nitrogen, and stored in liquid nitrogen until RNA extraction.

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