Ontology highlight
ABSTRACT:
PROVIDER: PRJNA391380 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:L. plantarum growth curve experiment sampled a different optical densities
| PRJNA146179 | ENA
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:DNA methylation is involved in many biological processes during plant growth and development. Here, we report a novel annual growth rhythm that is found in cotton plants grown in different time-of-year. To further study this rhythm in other plants, we use Arabidopsis thaliana for genome-wide bisulfite sequencing. Two A. thaliana DNA samples were extracted from 20 days old whole plant in Feburary and August for bisulphite treatment and further Illumina sequencing.
2013-07-21 | E-GEOD-38991 | biostudies-arrayexpress
Project description:ETEC is an important human pathogen. Although the mechanism of diarrhea is known in ETEC, the regulatory networks are less understood. This study was conducted to understand the global expression of ETEC isolate E24377A under different growth and environemental conditions. ETEC isolate E24377A was grown in the presence of several chemical signals, including bile salts, glucose, and pre-conditioned media (PCM) from other enteric pathogens. E24377A was also grown to different densities, to see if a quorum sensing mechanism was in place The isolate was grown in different types of media, with different ammendments, and at different growth densities. The overall goal was to determine how expression gene expression changes in the presence of chemical signals; a special emphasis was placed on the expression of known and suspected virulence and colonization factors
2012-03-01 | E-GEOD-31804 | biostudies-arrayexpress
Project description:With the quantitative profiling of consecutive tissue growth stages, we provide a global overview of expression changes of individual genes that play a role in dynamic cellular processes and developmental changes. We used tandem mass tag-based mass spectrometry and RNA sequencing to generate proteomic, phosphoproteomic and transcriptomic expression profiles for rosette leaf, flower and fruit tissue samples of the model plant Arabidopsis thaliana. In doing so, we have generated a multi-omics dataset of progressive changes during the development of three important plant organ types that can be used to study the underlying molecular mechanisms from different angles.
2020-09-15 | PXD018814 | Pride
Project description:DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue-specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition, we compared DNA methylation with tissue-specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots. No replicates, two libraries for root methylation.
2014-02-11 | E-GEOD-52762 | biostudies-arrayexpress
Project description:We sequenced mRNA of G. biloba leaves from different planting densities using the Illumina HiSeq4000 platform. We identified the transcriptome changes in leaves , which provided valuable information for uncovering the molecular mechanisms of flavonoid accumulation in G. biloba under different densities.
2021-06-05 | GSE176193 | GEO
Project description:We investigated how varying the composition of cell culture formulations and growing cancer cells at different densities might affect tumor cells genotype. Specifically, we compared gene expression profiles generated by human MDA-MB-231 human breast cancer cells cultured in different media (MEM, DMEM, or RPMI 1640) containing different concentrations of fetal bovine serum (FBS) or different sera (equine or bovine) that were grown at different cell densities.
2015-06-17 | GSE61670 | GEO