Ontology highlight
ABSTRACT:
PROVIDER: PRJNA788162 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples. We collected different tissue samples from the mature plants. Total RNA isolated from these tissue samples was subjected to Illumina sequencing. The sequence data was further filtered using NGS QC Toolkit to obtain high-quality reads. The filtered reads were used for de novo assembly optimization. The reads were further mapped to the Catharanthus transcripts via CLC Genomics Workbench and differential gene expression analysis was performed using DESeq software.
2014-07-29 | E-GEOD-57326 | biostudies-arrayexpress
Project description:We have performed gene expression profiling of surgically resected liver metastases by exon-resolution microarrays, and identified a metastasis-oriented subtyping framework consisting of 5 de novo transcriptomic subtypes (LMS1-5).
2021-07-27 | GSE159216 | GEO
Project description:In this study, we aim to present a global transcriptome analysis of medicinal plant, Catharanthus roseus. We generated about 343 million high-quality reads from three tissues (leaf, root and flower) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.
2014-07-29 | GSE57326 | GEO
Project description:In this study, we aim to present a global transcriptome analysis of medicinal/spice plant, Crocus sativus. We generated about 206 million high-quality reads from five tissues (corm, leaf, Tepal, stamen and stigma) using Illumina platform. We performed an optimized de novo assembly of the reads and estimated transcript abundance in different tissue samples. The transcriptome dynamics was studied by differential gene expression analyses among tissue samples.
2016-03-04 | GSE65103 | GEO
Project description:In this study, we performed de novo transcriptome assembly for L. japonica, representing transcripts from nine different tissues. A total of 22Gbps clean RNA-seq reads from nine tissues of L. japonica were used, resulting in 243,185 unigenes, with 99,938 unigenes annotated based on homology search using blastx against NCBI-nr protein database. Unsupervised principal component analysis and correlation studies using transcripts expression data from all nine tissues of L. japonica showed relationships between tissues explaining their association at different developmental stages. Homologs for all genes associated with chlorogenic acid, luteolin, and secoiridoid biosynthesis pathways were identified in the L. japonica transcriptome assembly. Expression of unigenes associated with chlorogenic acid were enriched in stem and leaf-2, unigenes from luteolin were enriched in stem and flowers, while unigenes from secoiridoid metabolic pathways were enriched in leaf-1 and shoot apex. Our results showed that different tissues of L. japonica are enriched with sets of unigenes associated with a specific pharmaceutically important metabolic pathways, and therefore, possess unique medicinal properties. Present study will serve as a resource for future attempts for functional characterization of enzyme coding genes within key metabolic processes. De novo transcriptome assembly and characterization, and transcriptome profiling for nine tissues of Lonicera japonica
2016-07-01 | E-GEOD-81949 | biostudies-arrayexpress
Project description:De novo Transcriptome Sequencing of the potent medicinal plant Piper chaba Hunt.
| PRJNA1097210 | ENA
Project description:The aim of this study is to identify alterations induced in gastric mucosa of mice exposed to Pteridium aquilinum and/or infected with Helicobacter pylori, in order to identify genes that are induced by bracken fern exerts exacerbating effects on gastric lesions associated to the infection. Six groups of C57Bl/6 mice were be used: 1) control, 2) infected Helicobacter pylori, 3) treated with Bracken fern extract orogastrically, 4) treated with Bracken fern extract in drinking water, 5) infected Helicobacter pylori + treated with Bracken fern extract orogastrically, 6) infected Helicobacter pylori + treated with Bracken fern extract in drinking water. The infection procedure was performed using an orogastric inoculation of H.pylori (strain SS1) twice in the first week. The RNA isolation was done in triplicate (3 mice per each condition). Further evaluation of morphological alterations on gastric mucosa, proliferative index and induction of DNA strand breaks will be performed in the mice stomach exposed to Pteridium aquilinum infected or not with Helicobacter pylori. Alterations of glycosylation in gastric tissues will also evaluated.
2011-09-07 | E-GEOD-31991 | biostudies-arrayexpress
Project description:De novo centromeres originate occasionally from non-centromeric regions of chromosomes, providing an excellent model system to study centromeric chromatin. The maize mini-chromosome Derivative 3-3 contains a de novo centromere, which was derived from a euchromatic site on the short arm of chromosome 9 that lacks traditional centromeric repeat sequences. Our previous study found that the CENH3 binding domain of this de novo centromere is only 288 kb with a high-density gene distribution with low-density of transposons. Here we applied next generation sequencing technology to analyze gene transcription, DNA methylation for this region. Our RNA-seq data revealed that active chromatin is not a barrier for de novo centromere formation. Bisulfite-ChIP-seq results indicate a slightly increased DNA methylation level after de novo centromere formation, reaching the level of a native centromere. These results provide insight into the mechanism of de novo centromere formation and subsequent consequences. RNA-seq was carried out using material from seedling and young leaves between control and Derivative 3-3. Bisulfite-ChIP-seq was carried out with anti-CENH3 antibodies using material from young leaves in Derivative 3-3.
2016-08-05 | E-GEOD-76533 | biostudies-arrayexpress
Project description:Regeneration is common in plants and transcription factors greatly contribute to this versatility of flowering plants; however, the evolution of this capability has hardly been explored. The callus can be induced from an intact plant rather than an explant in the water fern Ceratopteris richardii and the employed media are very different. The callus was verified having resulted in indirect de novo shoot organogenesis (IDNSO). Hundreds of genes were differentially expressed between the proliferating and the differentiating callus, hinting at significant changes in photosynthesis and hormone response. Many transcription factors were also differentially expressed, providing cues on how the callus proliferated and differentiated. STM-, ANT-, and ESE3-like transcription factor were simultaneously expressed in the vascular-initial-like cells in the callus, thus identifying a key tissue in callus differentiation; furthermore, they might have undergone subfunctionalization or neofunctionalization during evolution. Therefore, IDNSO was considered both conserved and diversified throughout vascular plants.
2022-09-09 | GSE212819 | GEO