Ontology highlight
ABSTRACT:
PROVIDER: PRJNA792564 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17335000_1.fastq.gz | Fastqsanger.gz | |||
| SRR17335000_2.fastq.gz | Fastqsanger.gz | |||
| SRR17335001_1.fastq.gz | Fastqsanger.gz | |||
| SRR17335001_2.fastq.gz | Fastqsanger.gz | |||
| SRR17335002_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 60 |
Similar Datasets
Project description:Protein kinases (PKs) are involved in plant growth and stress responses, and constitute one of the largest superfamilies due to numerous gene duplications. However, limited PKs have been functionally described in pecan, an economically important nut tree. Here, the comprehensive identification, annotation and classification of the entire pecan kinome was reported. A total of 967 PK genes were identified from pecan genome, and further classified into 20 different groups and 121 subfamilies using the kinase domain sequences, which were verified by the phylogenetic analysis. The receptor-like kinase (RLK) group contained 565 members, which constituted the largest group. Gene duplication contributed to the expansion of pecan kinome, 169 duplication events including 285 PK genes were found, and Ka/Ks ratio revealed they experienced strong negative selection. GO functional analysis indicated majority PKs involved in molecular functions and biological processes. The RNA-Seq data of PK genes in pecan were further analyzed at subfamily level, and different PK subfamilies performed various expression patterns across different conditions or treatments, suggesting PK genes in pecan involved in multiple biological functions and stress responses. Taken together, this study provided insight into the expansion, evolution and function of pecan PKs. Our findings regarding expansion, expression and co-expression analyses could lay a good foundation for future research to understand the roles of pecan PKs, and find the key candidate genes more efficiently.
2021-07-05 | GSE179336 | GEO
Project description:At 35 DAP whole kernels (pericarp + endosperm + embryo) without glumes of green house grown ears of heterozygous (+/bt2-H2328), self-pollinated plants were visually divided into pools of phenotypically normal looking kernels (small indentation, slightly smaller than mutant kernels, genotype +/+ or +/bt2-H2328) and pools of phenotypically mutant kernels (plump, round kernels, slightly larger than normal kernels, genotype bt2-H2328/bt2-H2328). Pools consisted of 4 kernels. 3 different ears were used for a biological duplicate. Keywords: gene knock out
2007-07-01 | GSE7030 | GEO
Project description:Incubation of physiologically dormant walnut kernels at warm and moist conditions leads to reduced germination and lower viability associated with triacylglycerol depletion, lipase activation and fatty acid accumulation. Cyanide however, releases kernel dormancy and improves germination accompanied with enhanced gluconeogenesis. The hypothesis that the viability loss in aging kernels is mainly due to lipid catabolism-induced oxidative stress and higher respiration was tested in a proteomic study. We used kernels with 15% moisture content aged by controlled deterioration, physiologically dormant non-aged and cyanide-treated germination primed; having low, medium and high germination potentials, respectively. We revealed 155 differentially abundant proteins out of 930 identified ones compared to dry (6% moisture content) kernels. Proteins accumulated in deteriorated kernels mainly belonged to protein folding, translation and degradation, defense, stress response and detoxification, glycolysis and fermentation but less abundant ones were related to gluconeogenesis and amino acid metabolism. Contrastingly, accumulated proteins belonged to gluconeogenesis and oxidative pentose phosphate pathway in germination-primed kernels. Deteriorated kernels also showed increased levels of H2O2, lipid peroxidation, free fatty acids, protein carbonylation, and amino acids, particularly proline but, a lower amount of sucrose and enhanced lipase, catalase, peroxidase and glutamate dehydrogenase activities. Of note, we revealed accumulation of various chaperons and proteins related to detoxification in deteriorated kernels, unlike reports on other aging seeds. Suppressed amino acid metabolism and gluconeogenesis enhanced respiration and oxidative stress in deteriorated kernels, while optimized carbon/energy metabolism promoted germination of primed kernels.
2024-02-23 | PXD040462 | Pride
Project description:At 35 DAP whole kernels (pericarp + endosperm + embryo) without glumes of green house grown ears of heterozygous (+/bt2-H2328), self-pollinated plants were visually divided into pools of phenotypically normal looking kernels (small indentation, slightly smaller than mutant kernels, genotype +/+ or +/bt2-H2328) and pools of phenotypically mutant kernels (plump, round kernels, slightly larger than normal kernels, genotype bt2-H2328/bt2-H2328). Pools consisted of 4 kernels. 3 different ears were used for a biological duplicate. Experiment Overall Design: 4 arrays - maize
2008-06-15 | E-GEOD-7030 | biostudies-arrayexpress
Project description:Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and during storage. Previous studies indicate that both constitutive and induced resistance are involved in maize kernel defense against A. flavus infection, little is known about molecular mechanisms of mature kernels in response to fungal infection. The purpose of this study is to determine gene expression differences in maize kernels between resistant and susceptible lines in response to A. flavus challenge. To avoid the environmental effects in the field inoculation, a laboratory based inoculation technique Kernel Screening Assay (KSA) was used to challenge kernels with A. flavus. After 72 hours incubation of inoculated and noninculated mature kernels, gene expression profiles of two Near Isogenic Lines (NIL) of Eyl25 (A. flavus resistant) and Eyl31 (A. flavus susceptible) were compared using oligonucleotide array.
2010-10-01 | GSE19883 | GEO
Project description:The objective of the current study is to unravel the gene regulatory networks controlled by the nkd genes during maize endosperm development. We compared wild type (B73) vs. nkd mutant (introgressed into B73 background) transcriptomes in aleurone vs. starchy endosperm cell types captured by laser capture microdissection technology. We performed RNA seq analysis of mid-mature (15DAP) endosperm in two cell types [aleurone (A) and starchy endosperm (S)] of wild type B73 (B) and nkd mutant (N) kernels with three independent biological replicates.
2015-01-28 | E-GEOD-61057 | biostudies-arrayexpress
Project description:Analysis of 35 mitochondrial genes expression level in dek53-ref and WT kernels at 15 days after pollination (DAP)
2020-01-01 | GSE141324 | GEO