IoArcGran
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB80828 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pocillopora grandis (antler coral), genomic and transcriptomic data
| PRJEB74266 | ENA
Project description:Eucalyptus species are widely used in the forestry industry, and a significant increase in the number of sequences available in database repositories has been observed for these species. In proteomics, a protein is identified by correlating the theoretical fragmentation spectrum derived from genomic/transcriptomic data against the experimental fragmentation mass spectrum acquired from large-scale analysis of protein mixtures. Proteogenomics is an alternative approach that can identify novel proteins encoded by regions previously considered as non-coding. This study aimed to confidently identify and confirm the existence of previously unknown protein-coding sequences in the Eucalyptus grandis genome.
2021-01-07 | PXD022110 | Pride
Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3â?¢6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq. Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance. Examination of mRNA levels in control and Al-treatment roots of C. grandis and C. sinensis with two biological replicates were generated by deep sequencing, using Illumina HiSeq 2000 device.
2016-08-24 | E-GEOD-85958 | biostudies-arrayexpress
Project description:Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation. Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field
2015-04-15 | E-GEOD-67873 | biostudies-arrayexpress
Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq. Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.
2016-08-24 | GSE85958 | GEO
Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in leaves by RNA-Seq. Results: Using RNA-seq, we isolated 1162 (181) up- and 496 (234) downregulated genes from Al-treated C. grandis (C. sinensis) leaves. Clearly, gene expression was less affected by Al-toxicity in C. sinensis leaves than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: ALUMINUM SENSITIVE 3 (ALS3), multidrug and toxic compound extrusion (MATE), glutathione S-transferase (GST), L-galactose dehydrogenase（L-GalDH) and lipoxygenase (LOX) were identified in citrus leaves. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus leaves. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.
2018-01-08 | GSE108837 | GEO
Project description:Gordius_albopunctatus, genomic and transcriptomic data
| PRJEB78907 | ENA
Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
2017-12-18 | PXD006238 | Pride
Project description:Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation.
2015-04-15 | GSE67873 | GEO