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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE30477 | GEO | 2011/09/15

SECONDARY ACCESSION(S): PRJNA143461

REPOSITORIES: GEO

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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. 10 dye-swap - genotype comparaison

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

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.

2011-05-12 | GSE28898 | GEO

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

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

Gene expression in hemera mutants in red light condition

Project description:The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22. Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4d. Seedlings were grown in constant red light (Rc, 10?mol/m2/s) at 21°C for 4d.

2014-06-01 | E-GEOD-43311 | biostudies-arrayexpress

cdka mutants-cdka mutants

Project description:rs10-06_cdka - cdka mutants - difference in global transcript in mutants with an affected cell cycle progression - compare wild type plants with mutant plants that show a reduced activity of CDKA1, the key cell cycle regulator in Arabidopsis thaliana

2012-03-20 | GSE36275 | GEO

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

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

della-regulation in darkness versus light-DELLAs contribute to skotomorphogenesis

Project description:rs09-09_della-dark - della-regulation in darkness versus light - Identification of DELLA-dependent downstream targets in darkness - Aim was to determine downstream target of DELLA proteins involved in skotomorphogenesis. Wt, ga1-3, ga1-3_rga_gai_rgl1_rgl2_rgl3 global seeds were sterilized, sown on MS agar plates then put for stratification for 3 days at 4°C. Plates were placed in growth cabinet at 22°C for 5 days in darkness or in continous light. Keywords: gene knock out

2011-06-13 | GSE22681 | GEO

cdka mutants-cdka mutants

2012-03-20 | E-GEOD-36275 | biostudies-arrayexpress

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

Project description:The RIP-seq experiment was designed to look for the direct targets of LSM4 U6snRNP component. For this plants were grown in Murashige and Skoog (MS) plates in continuous light (LL) for 12 days and were vacuum-infiltrated with 1% formaldehyde for 15 min followed by quenching with 125 mM glycine. A whole-cell extract was prepared in RIP-lysis buffer. The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap beads (Chromotek). After extensive washing with RIP washing buffer, co-precipitated RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

2023-05-31 | E-MTAB-12369 | biostudies-arrayexpress

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