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Small RNAs in Arabidopsis hybrid siliques

ABSTRACT: Five days post-fertilization siliques were collected for RNA extraction. After purification, small RNA libraries were generated for high throughput sequencing. Resulting sequences were analyzed to determine the contribution of the paternal genome to the small RNA transcriptome. Keywords: Epigenetics 4 unique samples. small RNAs purified from Arabidopsis siliques 5 days after pollination. Samples were selfed or hybrid crosses between ecotypes Columbia (Col) and Landsberg erecta (Ler).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Rebecca Mosher

PROVIDER: E-GEOD-15348 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis.

Mosher Rebecca A RA Melnyk Charles W CW Kelly Krystyna A KA Dunn Ruth M RM Studholme David J DJ Baulcombe David C DC

Nature 20090603 7252

Most eukaryotes produce small RNA (sRNA) mediators of gene silencing that bind to Argonaute proteins and guide them, by base pairing, to an RNA target. MicroRNAs (miRNAs) that normally target messenger RNAs for degradation or translational arrest are the best-understood class of sRNAs. However, in Arabidopsis thaliana flowers, miRNAs account for only 5% of the sRNA mass and less than 0.1% of the sequence complexity. The remaining sRNAs form a complex population of more than 100,000 different sma ...[more]

PMID: 19494814

Similar Datasets

Small RNAs in Arabidopsis hybrid siliques

Project description:Five days post-fertilization siliques were collected for RNA extraction. After purification, small RNA libraries were generated for high throughput sequencing. Resulting sequences were analyzed to determine the contribution of the paternal genome to the small RNA transcriptome. Keywords: Epigenetics

2009-03-24 | GSE15348 | GEO

sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

Project description:We examined sRNA populations in the Arabidopsis ecotypes C24, Landsberg erecta (Ler), and their reciprocal hybrids which display strong intra-species heterosis. The parental ecotypes had significant differences in their sRNA epigenomes and associated methylation profiles. The hybrids differed greatly from the parents in their sRNA epigenomes including a marked reduction in 24nt sRNA associated with loci that differed in the frequency of 24nt sRNAs between the parents.

2011-01-12 | GSE25022 | GEO

sRNA populations of 2 week old seedlings from Arabidopsis ecotypes C24, Ler, and their two reciprocal F1 hybrids

2011-01-12 | E-GEOD-25022 | biostudies-arrayexpress

Expression data for plant compensatory responses

Project description:Plant compensatory responses depends on transcriptional reprogramming. We used microarray analysis to understand the differential gene expression pattern between clipped (herbivore browsed) and unclipped plant. Arabidopsis ecotypes Columbia and Landsberg erecta were chosen due to their differential compensatory response. The plants were grown in greenhouse. At bolting stage the plants were clipped to imitate herbivore damage. Following day the samples were collected from clipped and unclipped plants.

2013-03-02 | E-GEOD-44781 | biostudies-arrayexpress

WGS of a serie of Arabidopsis thaliana tetrad's products to study the role of RECQ4A, RECQ4B, FIGL1 and FANCM genes in the rate, nature and distribution of meiotic recombination products (CO and NCO)

Project description:In this study, two accessions of Arabidopsis thaliana (Columbia and Landsberg erecta) were crossed and tetrads were obtained using thanks to the the quartet mutation, which keeps the 4 haploid pollen grains from a single meiosis attached together. By fertilising a plant (of ecotype Columbia) with a single tetrad, then selecting seeds from siliques containing exactly four seeds and finally sequencing the 4 developed plants, we can access the complete history of meiotic recombination events occurring in a single male meiosis. Comparison of the genomic sequences (WGS) of the 4 plants in a tetrad makes it possible to identify meiotic COs and NCOS events in each tetrad thanks to the numerous polymorphisms specific to each of the parental genomes. The analysis of the WGS tetrads data consists of genotyping a series of SNV markers (differentiating Columbia and Landsberg) positioned on the five chromosomes for the 4 (M1, M2, M3, M4) individuals of a tetrad, representing the 4 chromatids of each chromosomes. A total of 20 tetrads, the F1 and the two parental accessions Columbia and Landsberg erecta were sequenced.

2024-12-02 | E-MTAB-14435 | biostudies-arrayexpress

Transcription profiling of Arabidopsis ecotypes Landsberg erecta (Ler) and Landsberg to assess the effect of ERECTA on gene expression

Project description:To assess the effect of ERECTA on gene expression in Arabidopsis, genome wide transcript abundance was measured in Landsberg erecta (Ler) compared to Landsberg. For the differentially expressed genes, genetic variation in gene expression in the Ler/Cvi recombinant inbred line (RIL) population, resulted in the construction of a putative genetic regulatory network downstream of ERECTA.

2010-01-20 | E-TABM-627 | biostudies-arrayexpress

Identification of differentially expressed genes in brm-101 and syd-2 mutants

Project description:Global analysis of gene expression in 10 day old brm-101 and syd-2 mutant seedlings compared to wild type Landsberg erecta seedlings. Keywords: mutant analysis

2007-09-10 | GSE5806 | GEO

miRNA-Targeted and siRNA-Mediated mRNA Degradation Regulated by Argonaute, Dicer and RdRP

Project description:Microarray expression profiles of wild-type, ago1-10, ago1-11, and dcl1-9 Arabidopsis thaliana ec. Landsberg erecta seedling at 9, 21, and 35 days after germination. Keywords: mutant response

2006-05-17 | GSE4684 | GEO

Identification of LEAFY targets during reproductive transition

Project description:Global analysis of gene expression in 9 day old LEAFY-GR, 35S::LFY or Landsberg erecta seedlings treated with the steroid dexamethasone and/or the protein synthesis inhibitor cycloheximide. Keywords: other

2003-12-18 | GSE911 | GEO

The identification of novel genes involved in seed dormancy and after-ripening in Arabidopsis thaliana

Project description:We analysed the transcriptome of dormant and after-ripened imbibed seeds of different genotypes (Landsberg erecta and the different NILs) to identify dormancy and after-ripening genes that are absolutely required for these traits.

2017-08-21 | GSE90162 | GEO

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