Arabidopsis transparent testa 2 versus wild type
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: yongzhen pang
PROVIDER: E-MTAB-3659 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Comparison of Arabidopsis wild-type developing seeds grown under sulfur-deficient condition vs Arabidopsis wild-type developing seeds grown under control condition.
2007-06-01 | E-ATMX-1 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38018 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. microRNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38019 | biostudies-arrayexpress
Project description:We investigated RNA involved in the maternal control of progeny seed dormancy. Basically, we grew Ler wild type plants at 22 and 16 degree Celsius before fertilization which were moved to 22 degree for seed maturation along with ft-1 plants at 22 degree through lifetime (which show decreased seed germinability). Various RNA fractions were prepared from developing siluqes (seeds removed) and seeds, and sequenced to identify genes involved in transducing maternal memory of temperature to progeny seeds.
2014-11-20 | E-MTAB-2869 | biostudies-arrayexpress
Project description:merMEDEA (MEA) is a component of the Polycomb Repressive complex 2 (PRC2) of Arabidopsis thaliana, and a maternal imprinted gene that functions during central cell, embryo and endosperm development. Seeds that develop from mea mutant egg cells abort regardless of the paternal genotype. With this approach, we aim to uncover putative genes that are downstream of MEA and might cause the seed abortion phenotype. For this, we compare three developmental time point datasets between wild-type and mea mutant: ovary (before fertilization), and seed at 1-2 and 4 days after pollination (DAP).
2021-06-25 | E-MTAB-9569 | biostudies-arrayexpress
Project description:Comparison of seed of two different types of developing fruits in apple: central and lateral. Our objective is to find transcriptomic signatures that allow to explain the physiological drop of young lateral fruitlets Apple seeds transcriptomes were generated by deep sequencing by triplicate from seeds collected from central and lateral fruitlets at 20 days after petal fall (DAPF)
2014-11-21 | E-GEOD-62415 | biostudies-arrayexpress
Project description:Arabidopsis seeds expressing the castor fatty acid hydroxylase accumulate hydroxylated fatty acids up to 17% of total fatty acids in seed triacylglycerols, however total seed oil is also reduced up to 50%. Investigations into the cause of the reduced oil phenotype through in vivo [14C]acteate and [3H]2O metabolic labeling of developing seeds surprisingly revealed that the rate of de novo fatty acid synthesis within the transgenic seeds was approximately half that of control seeds. Addition of castor phospholipid:diacylglycerol acyltransferase (PDAT) increased hydroxylated fatty acid content of the seed oil, increased the rate of fatty acid synthesis, and mostly restored seed oil levels. RNAseq analysis indicated no changes in expression of fatty acid synthesis genes in hydroxylase-expressing plants. Transcript profiles of Arabidopsis developing seeds of three lines, at three stages of development were generated by deep sequencing, in triplicate, using Illumina.
2014-01-10 | E-GEOD-53952 | biostudies-arrayexpress
Project description:Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions. Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.
2010-07-08 | E-GEOD-18827 | biostudies-arrayexpress
Project description:In Brassicaceae and other species, the developing embryo develops in a spatially constrained environment, modulating embryo´s shape and size. It is unknown how embryonic cells adapt their growth and metabolism to the apparent mechanical cues, and in particular if embryo maturation is affected by physical constraints. To address this question, we performed topographical analysis (magnetic resonance imaging, infrared microspectroscopy, immunolabelling), metabolite, transcript and proteome profiling in developing seeds of Brassica napus. Here we describe how the imposition of mechanical stress during development causes a stimulation of oil and protein storage activity, characteristic of embryo maturation.
2024-08-01 | PXD027763 | Pride
Project description:Understanding the regulation of lipid metabolism is vital for genetic engineering of Brassica napus (B. napus) to increase oil yield or modify oil composition. We report the application of Illumina Hiseq 2000 for transcriptome profiling of seeds of B. napus at different developmental stages, which may uncover the dynamic changes in lipid metabolism and reveal key genes involved in lipid biosynthesis and degradation. Total RNA from developing seeds at 2, 4, 6, and 8 weeks after pollination (WAP) were isolated and sequenced separately. The gene expression levels of all samples were quantified and normalized by the DESeq normalization. We found that the biosynthesis of fatty acids is a dominant cellular process from 2 to 6 WAP, while the degradation mainly happens after 6 WAP. Two genes, encoding for acetyl-CoA carboxylase and acyl-ACP desaturase, might be critical for fatty acid biosynthesis in oil rape seeds. This study provides insight into the mechanism underlying lipid metabolism and reveals candidate genes that are worthy of further investigation for their values in genetic engineering of B. napus. Whole Transcriptome profiling of developing Brassica napus seeds at 2, 4, 6, 8 WAP by RNA sequencing using Illumina HiSeq 2000.
2016-02-06 | E-GEOD-77637 | biostudies-arrayexpress