Ontology highlight
ABSTRACT:
PROVIDER: PRJNA625414 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
2020-06-01 | MODEL2003240001 | BioModels
Project description:Purpose: Investigate genes associated to resistance of Xanthomonas perforans race T4 in tomato line with different resistance level Methods: Resistant and susceptible tomato breeding lines were subjected to the inoculation with Xanthomonas perforans race T4 followed by sample collection at 48 hpi and RNA-seq analysis for screening differential expressed genes associated with inoculation of pathogen. Results: Revealed gene expression profiles associated disease resistance and susceptiblilty.
2019-08-02 | GSE135232 | GEO
Project description:Long non-coding RNAs (lncRNA) constitute a large fraction of mammalian transcriptomes that still remains unexplored, mainly due to the lack of comprehensive, high-quality lncRNA annotation that limits the possibility to fully explore their functional capacity. We have developed RACE-seq, an experimental workflow based on RACE (Rapid Amplification of cDNA Ends) and long read RNA sequencing, aimed at both rare isoform discovery and better definition of gene boundaries. We applied 3â and 5â RACE-seq on 398 low-expressed GENCODE v7 lncRNA genes in seven human tissues (brain, testis, heart, kidney, liver, lung and spleen). The sequences obtained led to the discovery of 2,641 on-target, previously unknown alternative transcripts. Novel isoforms extended 60% of the 398 targeted lncRNA loci further in either 5' or 3', and often reached genome hallmarks typical of gene boundaries. In parallel, we used nested RACE-seq, and confirmed that nested RACE-seq has overwhelmingly better sensitivity than its standard counterpart.
2016-06-01 | E-MTAB-3912 | biostudies-arrayexpress
Project description:We investigated the toxicity of soil samples derived from a former municipal landfill site in the South of the Netherlands, where a bioremediation project is running aiming at reusing the site for recreation. Both an organic soil extract and the original soil sample was investigated using the ISO standardised Folsomia soil ecotoxicological testing and gene expression analysis. The 28 day survival/reproduction test revealed that the ecologically more relevant original soil sample was more toxic than the organic soil extract. Microarray analysis showed that the more toxic soil samples induced gene regulatory changes in twice as less genes compared to the soil extract. Consequently gene regulatory changes were highly dependent on sample type, and were to a lesser extent caused by exposure level. An important biological process shared among the two sample types was the detoxification pathway for xenobiotics (biotransformation I, II and III) suggesting a link between compound type and observed adverse effects. Finally, we were able to retrieve a selected group of genes that show highly significant dose-dependent gene expression and thus were tightly linked with adverse effects on reproduction. Expression of four cytochrome P450 genes showed highest correlation values with reproduction, and maybe promising genetic markers for soil quality. However, a more elaborate set of environmental soil samples is needed to validate the correlation between gene expression induction and adverse phenotypic effects.
2012-04-16 | GSE37154 | GEO
Project description:Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), termination sequencing (term-seq), ribosome profiling, and label-free shotgun proteomic mass spectrometry across different growth conditions to improve annotation and assign functional sites in the Z. mobilis genome. Proteomics and ribosome profiling informed revisions of protein-coding genes, which included 44 start codon changes and 42 added proteins.
2020-07-10 | PXD016962 | Pride
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
2023-12-31 | GSE155194 | GEO
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
2023-12-31 | GSE178993 | GEO
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
2023-12-31 | GSE178603 | GEO
Project description:LC-MS/MS data obtained from subglottic biopsies collected from 12 individuals with idiopathic subglottic stenosis, as well as 3 age-, sex-, and race/ethnicity-matched controls. All tissue donors were women of White race and non-Latino or Hispanic ethnicity. Sample preparation, mass spectrometry, and data analysis details are available in the published article.
2020-11-21 | MSV000086498 | MassIVE