Rice Raw Reads
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33943 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The SNP set of 94 rice representative species
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Project description:The SNP set of 94 rice representative species
| PRJEB33930 | ENA
Project description:Using the HiSeqTM 2000 sequencing platform, the anther transcriptome of photo thermo sensitive genic male sterile lines (PTGMS) rice Y58S and P64S (Peiâai 64S) were analyzed at the fertility sensitive stage under cold stress.These datas would be most beneficial for further studies investigating the molecular mechanisms of rice responses to cold stress.
2015-04-22 | E-MTAB-4312 | biostudies-arrayexpress
Project description:Morus alba L. Raw protein sequence reads and sequence
2024-02-08 | PXD049451 | iProX
Project description:Crown roots differentiate from stem base in rice. In this study, we followed gene expression in stem base of two Vietnamese indica rice varieties that belong to two haplotypes defining a QTL associated with crown root number. We used microarrays to look for the gene differentially expressed in stem base of two varieties.
2018-01-31 | GSE77130 | GEO
Project description:Roots make the first contact with the soil environment and are the first responders of stress. These root behaviors are quantifiable and adaptive. The response of rice varieties in mechanical and salinity stress was measured in a novel experimental setup that mimics the soil environment. We analyzed the response of roots by means of SAC (Stress Adaptation Coefficient) in 28 rice varieties that include high-yield salt tolerant varieties as well as geographically isolated native rice varieties. cDNA microarray of IR64 root-tip shows about 6000 common transcripts to be differentially regulated among the two stresses and common pathways were identified. Overall, our study indicates that there is an important commonality in the molecular basis of salt and mechanical stress and presents an easy-to-perform early establishment stress screen for rice varieties.
2018-12-20 | GSE117170 | GEO
Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.
2020-04-27 | PXD018338 | Pride
Project description:Abstract We have re-analysed publicly available mass spectrometry (MS) data sets enriched for phosphopeptides from Asian rice (Oryza sativa). In total we have identified, 15522 phosphosites on Serine, Threonine and Tyrosine residues on rice proteins. The data has been loaded into UniProtKB, enabling researchers to visualise the sites alongside other stored data on rice proteins, including structural models from AlphaFold2, and into PeptideAtlas, enabling visualisation of the source evidence for each site, including scores and source mass spectra. We identified sequence motifs for phosphosites, and link motifs to enrichment of different biological processes, indicating different downstream regulation caused by different kinase groups. We cross-referenced phosphosites against single amino acid variation (SAAV) data sourced from the rice 3000 genomes data, to identify SAAVs within or proximal to phosphosites that could cause loss of a particular site in a given rice variety. The data was further clustered to identify groups of sites with similar patterns across rice family groups, allowing us to identify sites highly conserved in Japonica, but mostly absent in, for example, Aus type rice varieties - known to have different responses to drought. These resources can assist rice researchers to discover alleles with significantly different functional effects across rice varieties.
2023-11-08 | PXD046188 | Pride
Project description:The genome structrure of domesticated species is influenced by complexity of breeding practices exercised by humans. Hokkaido is the northern-most regio of Japan, and one of northern limit of rice cultivation of world. The climatic conditions of Hokkaido are considered to be unsuitable for rice cultivation. Rice breeding programs of Hokkaido have focused on adaptability to specific local environmental condiitons (such as short growth period, low temperature conditions). These specific selection pressures have generated the unique genetic structures of Hokkaido rice cultivars. The genotype of sixty-three Hokkaido rice varieties were already analyzed by SSR marker, and the results showed that Hokkaido rice varieties were classified into six groups (Shinada et al, 2014). The unique genomic structures of six groups may have related to specific gene expression. This study analyze the gene expression profiles of Hokkaido rice variety.
2014-10-31 | GSE57645 | GEO
Project description:I'm a biochemist currently doing my PhD and the primary person involved in obtaining this data set.
I'm currently working with rice at the in vitro level, greenhouse controlled conditions and field trials. I am studying the proteome of salinity tolerant varieties, the implication of gibberellins in height and tolerance to salinity, and finally biotechnology to reduce the time to obtain stable hybrid rice lines.
| MSV000082921 | MassIVE