Triticum aestivum
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ABSTRACT:
PROVIDER: PRJNA111141 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Triticum aestivum cultivars Scorpion 25 and Xi 19 were grown under both normal and hot/dry conditions. We compared the effect of these two growth conditions on these two closely related varieties.
2008-09-20 | GSE12832 | GEO
Project description:Triticum aestivum cultivars Scorpion 25 and Xi 19 were grown under both normal and hot/dry conditions. We compared the effect of these two growth conditions on these two closely related varieties. We sequenced two biological replicates each for both Scorpion 25 and Xi19 grown under normal conditions. One library for hot/dry growth conditions was sequenced for each of these two cultivars.
2008-09-20 | E-GEOD-12832 | biostudies-arrayexpress
Project description:We have analyzed the pattern of gene expression in human primary CD34(+) stem/progenitor cells. We identified 42,399 unique serial analysis of gene expression (SAGE) tags among 106,021 SAGE tags collected from 2.5 x 10(6) CD34(+) cells purified from bone marrow. Of these unique SAGE tags, 21,546 matched known expressed sequences, including 3,687 known genes, and 20,854 were novel without a match. The SAGE tags that matched known sequences tended to be at higher levels, whereas the novel SAGE tags tended to be at lower levels. By using the generation of longer sequences from SAGE tags for gene identification (GLGI) method, we identified the correct gene for 385 of 440 high-copy SAGE tags that matched multiple genes and we generated 198 novel 3' expressed sequence tags from 138 high-copy novel SAGE tags. We observed that many different SAGE tags were derived from the same genes, reflecting the high heterogeneity of the 3' untranslated region in the expressed genes. We compared the quantitative relationship for genes known to be important in hematopoiesis. The qualitative identification and quantitative measure for each known gene, expressed sequence tag, and novel SAGE tag provide a base for studying normal gene expression in hematopoietic stem/progenitor cells and for studying abnormal gene expression in hematopoietic diseases. Keywords: other
2005-03-01 | GSE2346 | GEO
Project description:Comparison of gene expression levels in non-hardened (NH), cold-hardened (CH) and subzero-hardened (SZH) Triticum aestivum L. cv Jackson crowns with Affymetrix GeneChip Barley Genome Array. Keywords = wheat Keywords = crowns Keywords = cold tolerance Keywords = freezing resistance Keywords = Triticum aestivum L. cv Jackson Keywords: repeat sample
2005-01-20 | GSE2166 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus. Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-04-04 | GSE192518 | GEO
Project description:Accumulated evidence proves that mature spermatozoa contain a complex yet specific mRNA, which could provide information of the past events of spermatogenesis. Our aim was to quantitatively microdissect these mRNA transcripts by a digital approach. SAGE was used to study the mRNA transcripts from ejaculate of an individual and of a pool of 10 fertile men. SAGE library from individual produced 20237 raw tags representing 2459 unique tags (those tags that show at least twice in the library), and that from pooled 10 men generated 21052 raw tags representing 2712 unique tags. The SAGE view of ejaculate of fertile men has revealed a large number of transcripts, which occur in steady frequencies and probably have important implications in the spermatogenesis and fertilization. Keywords: normal gene expression profile
2005-11-11 | GSE3587 | GEO
Project description:Wheat (Triticum aestivum) was infiltrated with the Stagonospora nodorum effector protein SnTox3 to identify differentially regulated genes.
2014-07-25 | GSE59723 | GEO
Project description:Mass spectrometry-based wheat proteomics is challenging because the current interpretation of mass spectrometry data relies on public databases that are not exhaustive (UniProtKB/Swiss-Prot) or contain many redundant and poor or un-annotated entries (UniProtKB/TrEMBL). Here we report the development of a manually curated database of the metabolic proteins of Triticum aestivum (hexaploid wheat), named TriMet_DB (Triticum aestivum Metabolic Proteins DataBase). The manually curated TriMet_DB was generated in FASTA format, so that it can be read directly by programs used to interpret the mass spectrometry data. Furthermore, the complete list of entries included in the TriMet_DB is reported in a freely available resource, which includes for each protein the description, the gene code, the protein family,and the allergen name (if any). To evaluate its performance, the TriMet_DB was used to interpret the mass spectrometry data acquired on the metabolic protein fraction extracted from the MEC cultivar of Triticum aestivum.
2023-03-11 | PXD037709 | Pride
Project description:Two winter wheat cultivars possessing a high tolerance to Al (Triticum aestivum L. cv. Atlas66 and the near isogenic line OK91G106, named Century-T in this work [59]) and two winter wheat cultivars with low tolerance to Al (T. aestivum L. cv. Bounty and the near isogenic line OK91G108, named Century-S in this work [59]) were grown as previously described, and treated under conditions where Al remains mostly under the Al3+ form [10]. To reduce pH variations and ensure that Al speciation was stable throughout the experiment, at least 100 ml of solution was used for each plant. The root growth inhibition (RGI) is expressed as 100 × [1- (root growth of Al-treated seedling divided by the root growth of control seedlings)]. Root tips (5-10 mm) were isolated after 24 hours of exposure to Al and frozen on dry ice. Total RNA was isolated from the root tips (5 mm long) of 50 plants collected from the various genotypes using the RNeasy Plant Mini Kit (Qiagen). The RNA quality was assessed on agarose gels and with the Bioanalyzer 2100 (Agilent). Microarray profiling was performed according to Affymetrix protocols at the Functional Genomics Platform of the McGill University and Génome Québec Innovation Centre using the Affymetrix GeneChip Wheat Genome Array. Plants of the different lines were treated with Al concentrations resulting in 50% RGI: 50 ?M for the tolerant cultivars Atlas66 and Century-T and 5 ?M for the sensitive cultivars Bounty and Century-S. Three biological replicates were used and the results were analyzed using the Robust Multiarray Analysis (RMA version 0.2) freeware. Atlas66 and Bounty plants not exposed to Al were used as control for all the other conditions. Genes showing a differential expression greater than two-fold (RMA differential expression of log2 ? 1) between the Atlas66 and Bounty controls were excluded from the reference set as these may represent cultivar dependent differences in basal expression levels that could bias the analysis. Overall, this excluded 1.26% of the genes on the microarray (773 of 55,052) demonstrating that most genes are expressed at a similar level between the two cultivars. The microarray headings are the following : For each array headings: The first term represents the cultivar: A = Atlas66; B = Bounty, 106 = Century-T, 108 = Century-S. The second twerm represents the Al concentration: 0 = no aluminum 5 = 5 ?M aluminum and 50 = 50 ?M aluminum. The last term represents the sample replicate number S1, S2 or S3.
2008-06-30 | E-TABM-454 | biostudies-arrayexpress
Project description:We report a time series RNA-seq experiment involving two isolates of Puccinia graminis separately infecting Triticum aestivum cv. Morocco points post inoculation
2016-12-31 | GSE93015 | GEO