Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA134143 | ENA |
REPOSITORIES: ENA
Similar Datasets
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.
2010-12-01 | GSE25404 | GEO
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
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
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. Seeds of a DCL1/dcl1-15 plant were sown. For each wild-type sample, 300 torpedo stage embryos were selected from wild-type siblings. For each mutant replicate, 300 dcl1-15/dcl1-15 embryos were selected from the siliques of DCL1/dcl1-15 where the wild-type embryos were at the torpedo stage.
2011-02-17 | E-GEOD-24887 | biostudies-arrayexpress
Project description:Expression data of wild-type and dcl1-15 torpedo-staged embryos
| PRJNA132035 | ENA
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
Project description:mRNA sequencing of wild type Columbia and serrate-1 globular stage embryos of Arabidopsis thaliana
| PRJNA391826 | ENA
Project description:Deep-sequencing of total RNA from manually dissected wild-type Arabidopsis embryos at the globular stage
| PRJNA148157 | ENA
Project description:SuperSeries contain expression data from the nuclei of cell types involved in patterning events, with focus on root apical stem cell formation, at 16-cell stage, early globular stage and late globular stage in the early Arabidopsis embryo (atlas). Expression data comparing nuclear and cellular RNA isolated from whole 16-cell stage Arabidopsis embryos is also included. This SuperSeries is composed of the SubSeries listed below.
2017-11-06 | GSE89101 | GEO
Project description:Transcriptomics analysis of developing wild type and val1 mutant Arabidopsis embryos
| PRJNA301162 | ENA