Sequencing of Acetolactate Synthase from Representative Poaceae
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ABSTRACT:
PROVIDER: PRJEB31633 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Illumina RNA Sequencing (RNA-Seq) of Oryza sativa, Nipponbare for the Conserved Poaceae Specific Genes project. Authors: Robin Buell, Ning Jiang, Haining Lin, Rebecca Davidson, Malali Gowda, John Hamilton, Brieanne Vaillancourt
2012-04-04 | E-MTAB-2039 | biostudies-arrayexpress
Project description:This experiment highlights the extreme sequence bias generated by standard PCR amplication of sequencing libraries and decribes an adapted T7-polymerase based amplification method, which results in non-baised, representative libraries for Illumina sequencing Adaptation of standard Illumina sequencing protocol to obtain representative sequencing libraries after sample amplification. Comparing different amplification methods with amplification free sequencing.
2010-10-28 | E-GEOD-23868 | biostudies-arrayexpress
Project description:This experiment highlights the extreme sequence bias generated by standard PCR amplication of sequencing libraries and decribes an adapted T7-polymerase based amplification method, which results in non-baised, representative libraries for Illumina sequencing
2010-10-28 | GSE23868 | GEO
Project description:Leymus chinensis strain:Poaceae Transcriptome or Gene expression
| PRJNA230274 | ENA
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4401 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4401/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4400 | biostudies-arrayexpress
Project description:The Poaceae family, also known as the grasses, includes agronomically important cereal crops such as rice, maize, sorghum, and wheat. Previous comparative studies have shown that much of the gene content is shared among the grasses; however, functional conservation of orthologous genes has yet to be explored. To gain an understanding of the genome-wide patterns of evolution of gene expression across reproductive tissues, we employed a sequence-based approach to compare analogous transcriptomes in species representing three Poaceae subgroups including the Pooideae (Brachypodium distachyon), the Panicoideae (sorghum), and the Ehrhartoideae (rice). Our transcriptome analyses reveal that only a fraction of orthologous genes exhibit conserved expression patterns. A high proportion of conserved orthologs include genes that are upregulated in physiologically similar tissues such as leaves, anther, pistil, and embryo, while orthologs that are highly expressed in seeds show the most diverged expression patterns. This experiment is related to E-MTAB-4400 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4400/) and E-MTAB-4402 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-4402/)
2012-04-04 | E-MTAB-4401 | biostudies-arrayexpress
Project description:We report the application of sequencing-by-synthesis technology for high-throughput profiling of small RNAs involved in Chalcone synthase A (CHS-A) sense cosuppression in petunia. Sense cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a transgene overexpressing the host Chalcone Synthase-A (CHS-A) gene caused the degradation of the homologous transcripts and the loss of flower pigmentation. Though sense cosuppression is recognized as an RNA silencing mechanism, little evidence has been yet provided demonstrating its association with the generation of individual small interfering RNAs (siRNAs) that are the assumed determinants. In this work, the deep sequencing of small RNAs in cosuppressed transgenic petunia and WT petunia respectively allowed for the identication of siRNAs that vastly predominate in the silenced flower and guide prominent cleavage events in CHS-A mRNA. Examination of 2 small RNA populations from WT and cosuppressed petunia petals respectively
2009-09-27 | E-GEOD-13764 | biostudies-arrayexpress
Project description:All plants in this file are poaceae and data for these plants are contributed to the MSSATplant project and these data are fully publicly available. The mass spectrometry data were obtained in DDA mode, with the negative.
2022-12-07 | MSV000090857 | MassIVE
Project description:We report the application of sequencing-by-synthesis technology for high-throughput profiling of small RNAs involved in Chalcone synthase A (CHS-A) sense cosuppression in petunia. Sense cosuppression is a classical form of eukaryotic post-transcriptional gene silencing. It was first reported in transgenic petunia, where a transgene overexpressing the host Chalcone Synthase-A (CHS-A) gene caused the degradation of the homologous transcripts and the loss of flower pigmentation. Though sense cosuppression is recognized as an RNA silencing mechanism, little evidence has been yet provided demonstrating its association with the generation of individual small interfering RNAs (siRNAs) that are the assumed determinants. In this work, the deep sequencing of small RNAs in cosuppressed transgenic petunia and WT petunia respectively allowed for the identication of siRNAs that vastly predominate in the silenced flower and guide prominent cleavage events in CHS-A mRNA.
2009-09-28 | GSE13764 | GEO
Project description:Ectopic ATP synthase is a functional onco-protein increases cell proliferation when transported to plasma membrane of cancer cells. Our previous study performed large scale gene silencing screening indicated ER and mitochondrial transport pathways may lead to ectopic ATP synthase expression. Silencing dynamin-related protein 1 (Drp1), mitofusin-1 (Mfn1) and Parkin affected ectopic ATP synthases expression. However, the underlying trafficking mechanism is poorly understood. Here, we analyzed our membrane and mitochondrial proteome of lung cancer A549 cells and found that both nuclear-encoded ATP synthase subunits and mitochondrial-encoded components-ATP6 translocated to cell surface, indicating that ATP synthase subunits assembled in mitochondria. Furthermore, serum starvation enhanced ATP synthase translocation to plasma membrane, Mdivi-1, a chemical inhibitor of the mitochondrial fission protein Drp1, rescued the phenomena. Additionally, image quantification of mitochondria, showing that mitochondrial fission preference cells expressed more eATP synthase. Therefore, we proposed that eATP synthase trafficking may be related to mitochondrial dynamics. Additionally, ICC and flow cytometry revealed the expression of a critical transcription factor associated with high-risk neuroblastoma, MYCN, correlated with eATP synthase expression. To better understand whether MYCN mediated mitochondrial fission and affected ATP synthase trafficking, we first analyzed MYCN ChIP-sequencing data and found Drp1, Mfns and Parkin possessed the consensus DNA-binding motif of MYCN. Further high-resolution image analysis showed higher mitochondrial fission and eATP synthase expression in MYCN-amplified neuroblastoma. Last, silencing MYCN reduced the fission level by detecting DRP1. In summary, we suggest that trafficking of ectopic ATP synthase may via mitochondrial dynamics.
2023-05-10 | PXD007036 | Pride