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Transcript profiling of wild-type and dcl1-5 early globular embryos

ABSTRACT: DICER-LIKE1 (DCL1) is required for miRNA biogenesis and embryonic pattern formation. Presumably the patterning defects observed in dcl1-5 null embryos are due to the loss of miRNAs and the consequent up-regulation of their respective targets. To test which miRNA targets were up-regulated in dcl1 embryos relative to wild-type embryos, we performed genome-wide transcript profiling of wild-type and dcl1-5 early globular embryos using directional mRNA-Seq.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE25404 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA134143

REPOSITORIES: GEO

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Transcript profiling of wild-type and dcl1-5 early globular embryos

Project description:DICER-LIKE1 (DCL1) is required for miRNA biogenesis and embryonic pattern formation. Presumably the patterning defects observed in dcl1-5 null embryos are due to the loss of miRNAs and the consequent up-regulation of their respective targets. To test which miRNA targets were up-regulated in dcl1 embryos relative to wild-type embryos, we performed genome-wide transcript profiling of wild-type and dcl1-5 early globular embryos using directional mRNA-Seq. For RNA isolation, pools of 30 Col-0 (wild-type) and dcl1-5 early globular embryos were hand-dissected in water, immediately transferred to 30 ul of RNAlater (Ambion), incubated at 60M-BM-0 C with 500 ul TRIzol Reagent (Invitrogen) for 30 minutes, and then purified according to the TRIzol Reagent protocol for RNA isolation from small quantities of tissue (Invitrogen). Two rounds of linear amplification of poly(A) RNA were performed using the Arcturus RiboAmp HS Plus kit (Molecular Devices). Strand-specific mRNA-Seq libraries were generated as previously described (Guo et al., Nature, 2010). After removing adaptor sequences, sequences were mapped to the Arabidopsis thaliana genome (TAIR9 assembly) using the Bowtie short read aligner allowing up to two mismatches within a 25 nt M-bM-^@M-^XseedM-bM-^@M-^Y sequence and retaining reads mapping uniquely to the genome. Since the Arcuturus RiboAmp HS Plus kit generates amplified RNAs in the antisense orientation, reads were counted as matching TAIR9 annotated genes if they overlapped the antisense strand.

2010-12-01 | E-GEOD-25404 | biostudies-arrayexpress

Expression data of wild-type and dcl1-15 torpedo-staged embryos

Project description:Severe loss-of-function alleles of DCL1 are embryonic lethal. Defects in cell division were seen as early as the globular stage in the strong loss-of-function allele dcl1-15. Phenotypic work with dcl1-15 and the null allele dcl1-5 suggested that, in addition to the severe patterning defects, the mutants were maturing earlier than wild-type embryos. We performed global gene expression analysis of dcl1-15 and wild-type torpedo staged embryos to examine this maturation phenotype further. The results suggested that DCL1 is a heterochronic gene. Comparisons to a time series of embryo development (http://www.seedgenenetwork.net/arabidopsis) showed that the genes differentially expressed in dcl1-15 embryos behaved more like green-cotyledon stage embryos than torpedo embryos.

2011-02-17 | GSE24887 | GEO

Expression data of wild-type and dcl1-15 torpedo-staged embryos

2011-02-17 | E-GEOD-24887 | biostudies-arrayexpress

Investigation of small RNA and RNA-seq transcripts from soybean (Glycine max) DCL1 mutants

Project description:In plants, DICER-LIKE1 is a critical enzyme in the biogenesis pathway of plant miRNAs. Zinc-finger nucleases were used to generate single and double-mutants of soybean DCL1 homologs. We created several small RNA libraries to investigate the effect on miRNA abundance in these various mutants. RNAseq transcript data was also generated in order to investigate targets of those impacted miRNAs.

2016-03-04 | GSE76036 | GEO

mRNA sequencing of wild type Columbia and serrate-1 globular stage embryos of Arabidopsis thaliana

Project description:Wild type Columbia and serrate-1 globular stage embryos were sequenced in order to profile miRNAs which are expressed in embryogenesis in Arabidopsis thaliana

2017-06-27 | GSE100450 | GEO

Arabidopsis thaliana

Project description:Transcript profiling of wild-type and dcl1-5 early globular embryos

| PRJNA134143 | ENA

Expression data from Arabidopsis seed compartments at the pre-globular stage

2008-08-12 | GSE12402 | GEO

Transcription profiling of Arabidopsis seed compartments at the pre-globular stage

Project description:We collected pre-globular stage seed compartments from 7-micron paraffin sections using the Leica LMD6000 system in order to identify the mRNAs present in different compartments of seeds containing pre-globular-stage embryos was identified as those seeds containing embryo propers made up of between 2 and 8 cells. For the purposes of this study we captured 6 compartments: embyro proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, chalazal seed coat and general seed coat. Serial sections of entire seeds were also captured for comparison. Experiment Overall Design: Pre-globular stage seed compartments or whole seeds were isolated using the LMD6000 system. Total RNA was amplified and hybridized with Affymetrix ATH1 Arabidopsis array for 14 samples (embryo proper, micropylar endosperm, peripheral endosperm, chalazal endosperm, general seed coat, chalazal seed coat, whole seeds, 2 biological replicates each).

2008-10-21 | E-GEOD-12402 | biostudies-arrayexpress

Characterization of the starvation response in the Arabidopsis dcl1-9 mutant

Project description:The SnRK1 protein kinase, the plant ortholog of mammalian AMPK and yeast Snf1, is activated by the energy depletion caused by adverse environmental conditions. Upon activation, SnRK1 triggers extensive transcriptional changes to restore homeostasis and promote stress tolerance and survival partly through the inhibition of anabolism and the activation of catabolism. Despite the identification of a few bZIP transcription factors as downstream effectors, the mechanisms underlying gene regulation, and in particular gene repression by SnRK1, remain mostly unknown. microRNAs (miRNAs) are 20-24nt RNAs that regulate gene expression post-transcriptionally by driving the cleavage and/or translation attenuation of complementary mRNA targets. In addition to the well-established role of miRNAs as regulators of plant development, mounting evidence implicates miRNAs in the response to environmental stress. Given the involvement of miRNAs in stress responses and the fact that some of the SnRK1-regulated genes are miRNA targets, we postulated that miRNAs drive part of the transcriptional reprogramming triggered by SnRK1 activation. To test this we have performed comparative analyses of the transcriptional response to energy deprivation between WT and dcl1-9, a mutant deficient in miRNA biogenesis. To assess the impact of miRNA deficiency on the starvation response we performed transcriptomics analyses of WT and dcl1-9 plants by subjecting leaves to 6h of light (control) or darkness (starvation)

2013-07-15 | E-GEOD-46713 | biostudies-arrayexpress

Expression data from SRB embryo regions at the globular stage

Project description:We microdissected each embryo region from 6-micron paraffin sections using the Leica AS LMD system to identify all genes active in different embryo region of an SRB seed containing globular-stage embryos. Keywords: cell type comparison

2007-04-27 | GSE7592 | GEO

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