Ontology highlight
ABSTRACT:
PROVIDER: PRJNA827463 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25424617_1.fastq.gz | Fastqsanger.gz | |||
| SRR25424617_2.fastq.gz | Fastqsanger.gz | |||
| SRR25424618_1.fastq.gz | Fastqsanger.gz | |||
| SRR25424618_2.fastq.gz | Fastqsanger.gz | |||
| SRR25424619_1.fastq.gz | Fastqsanger.gz |
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Project description:An overview of the expression pattern of all rice genes under natural field conditions based on microarray analysis of different organs and tissues at various stages of growth and development from transplanting to harvesting. A total of 48 samples representing organs/tissues at various stages of growth and development with 3 replicates each except for one anther sample with 2 replicates. Vegetative organs such as leaf blade, leaf sheath, root and stem were sampled during the vegetative, reproductive and ripening stages. Young inflorescence, anther, pistil, lemma, palea, ovary, embryo, and endosperm were sampled at various stages of development.
2011-01-13 | E-GEOD-21396 | biostudies-arrayexpress
Project description:This study was initiated with the objective of identifying the anther/tapetum specific promoters from cotton floral buds. Cotton is an important commercial crop. Hybrid cotton varieties are developed to obtain improved yield and fiber quality. Most of the hybrid seed production in cotton is carried out by hand emasculation, which requires large amount of manpower, resulting in high cost of hybrid seed. We are developing barnase-barstar based male sterility system, which would be a better alternative for hybrid development. The tapetum specific promoters are main requirement for such a system. The study was thus carried out to identify genes expressed in the anthers. Cotton bud sizes were correlated with tapetum development. RNA was isolated from following tissues: • Anther tissues from buds at pre-meiotic stage of development (Tapetum absent) • Buds without anther tissues at pre-meiotic stage of development • Anther tissues from buds during meiosis (Tapetum present) • Buds without anther tissues during meiosis • Anther tissues from buds at post-meiotic stage of development (Tapetum degenerated) • Buds without anther tissues at post-meiotic stage of development • Leaf tissues • Seedling 5 days after germination Biotin labeled cRNA was hybridized on Affymertix cotton Genechip Genome array following Affymetrix protocols. Three biological replicates were maintained.
2013-10-31 | E-GEOD-51779 | biostudies-arrayexpress
Project description:Kumquat (Fortunella classifolia Swingle) was thought as a close relative to citrus according to fruit morphology taxonomic, but kumquat fruit as well as its flowering characteristic are distinct from other citrus species, the trees usually blooms on the medium of June, obviously later than other citrus species, moreover many kumquat accessions could be blossom more than one times during one growth season, as this reason, the kumquat fruits could be consecutively ripen over several months, which made the study of globe genes expression profile for different development stage fruit easy. Kumquat is non-climacteric fruit, however the kumquat fruit ripening process, especially genes expression change in young and ripe kumquat fruits are less known, so studying on the global genes expression profiles of kumquat fruits in young and ripe stage are especially helpful to identify ripening-related genes and unravel the mechanism of ripening process.
2013-11-25 | E-MTAB-1837 | biostudies-arrayexpress
Project description:Purpose: The chloroplast DNA has not been primiarly analyzed in rice plants before. Hence, the objective of this study is to analyze and compare the differential methylation of chloroplast DNA in MR219 indica rice across different tissues and different developmental stages. Methods: We prepared a total of nine sodium bisulfite treated DNA libraries from three developing grain tissues, three leaf tissues at ripening stage and three leaf tissues at vegetative stage and sequenced them in Illumina Miseq platform. We performed quality trimming, alignment followed by methylation calling and differential methylation analysis using Trimmomatic v36, Bismark v16.3 and SeqMonk v40.0 on the sequencing data obtained. Statistical analysis was carried out in SeqMonk software and further validated in SPSS statistical software v22.2. Results: With an optimized data analysis workflow, we mapped around average of 26000 reads to chloroplast genome. Differential CpG and CHG methylation in SeqMonk v40.0 revealed that MR219 chloroplast DNA is differentially methylated in grain and leaf tissues and across vegetative stage and ripening stage in the leaf tissues. Chloroplast DNA from leaf at ripening stage was most methylated, followed by grain tissue and lastly leaf tissue from vegetative stage. Conclusions: Overall, it can be concluded that the organellar DNA in MR219 rice are differentially methylated at different tissues and across different developmental stages. The chloroplast DNA was most methylated in the leaf at ripening stage, followed by grain at ripening stage and leaf at vegetative stage. The functional significance of the differential methylation observed in this study needs to be investigated.
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