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Comparison of IND induced vs. mock treated seedlings: Transcriptome profiling upon induction of the transcription factor IND

ABSTRACT: rs10-03_ind - comparison of ind induced vs mock treated seedlings - Identification of miRNAs regulated by IND - Transgenic seeds containing an IND transgene under the control of a dexamethasone inducible promoter were germinated and grown in liquid Murashige/Skoog medium under a 16h light/8h darkness light regime. After seven days of growth, seedlings were either mock-treated or treated with 10 micromolar dexamethasone for 24 hours.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE28898 | GEO | 2011/05/12

SECONDARY ACCESSION(S): PRJNA140653

REPOSITORIES: GEO

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Comparison of IND induced vs. mock treated seedlings: Transcriptome profiling upon induction of the transcription factor IND

Project description:rs10-03_ind - comparison of ind induced vs mock treated seedlings - Identification of miRNAs regulated by IND - Transgenic seeds containing an IND transgene under the control of a dexamethasone inducible promoter were germinated and grown in liquid Murashige/Skoog medium under a 16h light/8h darkness light regime. After seven days of growth, seedlings were either mock-treated or treated with 10 micromolar dexamethasone for 24 hours. 3 dye-swap - induced vs non-induced comparison

2011-05-12 | E-GEOD-28898 | biostudies-arrayexpress

An essential role for cullin 3 ubiquitin ligases and phototropin 2 turnover in seedling chloroplast development (de-etiolation)

Project description:Transgenic Arabidopsis seedlings RV86-5 (contains a dexamethasone-inducible ubiquitin variant that contains Arg instead of Lys at position 48; ̈Schlögelhofer et al., 2005) were surface-sterilized and sown on Uhelon 120T (Silk & Progress, Czech Republic) mesh placed on 1% (w/v) agar containing a half-strength Murashige and Skoog medium (pH 5.7), stratified at 4 °C for 3 d, and cultivated at 21 °C/19 °C day/night temperatures, with a 16 h photoperiod (90 μmol m−2 s−1 light intensity) for 14 d. On the fourteenth day (after the first 2 h of the day period), the Uhelon mesh with the seedlings was transferred onto a new solid medium supplemented with (i) 5×10−4% (v/v) DMSO (mock); (ii) 0.7 or 7.0 μM dexamethasone (DEX) and rinsed with DMSO or DEX-supplemented water for mock and DEX-treated seedlings, respectively, and incubated for 24 hours.

2022-05-04 | PXD012815 | Pride

comparison of transcriptomes in mad mutants-Transcriptome analysis of miRNA action deficient mutants

Project description:rs10-04_mad - comparison of transcriptomes in mad mutants - What gene sets are differentially expressed in mad mutants? - Seeds of GFP171.1 (parental line), mad1, mad2, mad3, mad6 and dcl1-12 were sterilized and germinated on Murashige/Skoog medium with 0.9% agar. Plates were stratified at 4C in the dark for 4 days. The plates were then transferred to a growth cabinet at 21C under a 16h light/8h darkness light regime, and the seedlings were harvested 18 days after transfer to the growth cabinet.

2011-09-15 | GSE30477 | GEO

Transcriptome analysis of genes regulated by INDEHISCENT (IND) transcription factor under the control of the 35S promoter after treatment with auxin

Project description:IND is a regulator of fruit development in Arabidopsis thaliana. To identify genes regulated by IND we performed array based transcriptome analysis of Dexamethasone (DEX) inducible IND transgenic seedlings. One week old 35S::IND:GR seedlings were treated with DMSO, Auxin, DEX and Auxin plus DEX for 6 h. Three biological independent experiments were performed.

2017-07-05 | E-MTAB-3812 | biostudies-arrayexpress

comparison of transcriptomes in mad mutants-Transcriptome analysis of miRNA action deficient mutants

2011-09-14 | E-GEOD-30477 | biostudies-arrayexpress

Transcription profiling of Arabidopdis seedlings - heat, anoxia, and combined heat-anoxia treatments

Project description:Anoxia induces several heat shock proteins and a heat pre-treatment can acclimatize Arabidopsis seedlings to a subsequent anoxic treatment. In this work we analyzed the response of Arabidopsis seedlings to anoxia, heat and a combined heat+anoxia stress. A significant overlapping between the anoxic and heat shock responses has been observed by whole-genome microarray analysis. Experiment Overall Design: We treated Arabidopsis seedling, 4-days old, dark germinated with: Experiment Overall Design: -Control (23Â°C, dark, liquid Murashige-Skoog medium containing 30mM sucrose). Experiment Overall Design: -Heat-treated (38Â°C for 90 minutes, dark, liquid Murashige-Skoog medium containing 30mM sucrose). Experiment Overall Design: -Anoxia-treated (23Â°C, under anoxia for 6h, dark, liquid Murashige-Skoog medium containing 30mM sucrose). Experiment Overall Design: -combined heat+Anoxia-treatment (23Â°C, treated at 38Â°C for 90 min and thereafter under anoxia for 6h, dark, liquid Murashige-Skoog medium containing 30mM sucrose). Experiment Overall Design: Two biological replicates for each condition.

2009-06-08 | E-GEOD-16222 | biostudies-arrayexpress

Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response

Project description:To analyze the extent of the overlap between MeJA-induced transcripts and MeJA- induced histone acetylation, the expression profiles of WT untreated (WT), WT+MeJA, axe1-5 untreated and axe1-5+MeJA samples were analysed using the catalog microarray (Agilent design ID:21169). Whole A. thaliana seedlings of axe1-5 mutant and DR5 wild-type lines (Murfett et al 2001) were grown in vitro for 12 days on 1% Murashige and Skoog (MS) medium (Duchefa) supplemented with 1% sucrose, 0.8% phytoagar (Duchefa) and buffered to pH 5.8. Stratification of seeds was performed for 3 days at 4°C in the dark. Seeds were then grown with plates approximately 20° to vertical under 16h light/8h dark cycles for 12 days at 22°C and a light intensity of 100-120 µmol m-2s-1. Twelve-day-old in vitro grown whole seedlings were transferred to 50 µM MeJA or mock plates and sampled after 3 hours for microarray analysis. Expression profiles were analyzed using the catalog microarray (Agilent design ID:21169).

2022-04-11 | GSE162891 | GEO

RNA-seq experiment to evaluate the role of methylation of the spliceosome component LSM4 in the regulation of alternative splicing

Project description:The RNA-seq experiment looks for the role of methylation in the control of alternatives. Wild-type, lsm4-1, LSM4R and LSM4RxK in lsm4-1 background seedlings were grown on Murashige and Skoog (MS) medium containing 0.8% (w/v) agar for 12 days under continuous light at 22°C. Three biological replicates were collected. Whole seedlings were harvested and total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate RNA concentration NanoDrop 2000c (Thermo Scientific) was used. Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

2023-05-31 | E-MTAB-12370 | biostudies-arrayexpress

Transcription profiling by array of control and TCP13-SRDX transgenic Arabidopsis plants

Project description:To understand the downstream genes of TCP13, we performed analysis of gene expression using vector control plants and the TCP13 fused repression domain plants (TCP13pro::TCP13SRDX) . TheTCP13pro::TCP13SRDX plants is transgenic plants expressing chimeric repressor (SRDX) fused to TCP13 cDNA using the TCP13 promoter. TCP13 is a drought-inducible gene and play an essential role in leaf morphology. Arabidopsis plants were grown on the Murashige and Skoog (MS) medium (Murashige and Skoog, 1962), supplemented with 3% sucrose and 0.8 % agar (under a 16-h-day (60 ± 10 μmol photons m−2 s−1 light intensity) and 8-h-night regime for 2 weeks.

2023-07-07 | E-MTAB-9336 | biostudies-arrayexpress

Transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt and ER-stress

Project description:Grapevine rootstock 1616C shoots were sterilized and cultured on Murashige & Skoog (MS) medium containing 2% sucrose (w/v). Plantlets were grown in a growth chamber with a 16-h light/8-h dark cycle for 10 weeks at 25 °C. Plantlets with 4–5 leaves were chosen for use in stress treatments. Experiments were conducted with treatment groups: The control (C, without any chemical treatment), TM (treated with 5 μg mL-1 tunicamycin (TM)) and salt (treated with 400 mM NaCl). Microarray analysis was performed and we investigated transcript profiles in leaves of the salt-tolerant grapevine rootstock 1616C under salt- and ER-stress at 6 and 24 hours

2020-07-10 | GSE150581 | GEO

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