Similar Datasets
Project description:To further verify the differences in IncRNA and miRNA during radish flowering, we conducted transcriptome analysis on samples taken before and after radish flowering. Obtain IncRNA and miRNA from the differential table and perform qRT-PCR validation on them.
2024-03-14 | GSE261303 | GEO
Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7. Eleven different conditions were sequenced on the SOLiD system. Of two of the condtions, spinach medium and LB-nitrite, technical replicates were sequenced. Of LB medium and radish sprouts, biological replicates were sequenced on an Illumina MiSeq.
2014-07-20 | E-GEOD-48199 | biostudies-arrayexpress
Project description:We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".
2021-08-31 | GSE182885 | GEO
Project description:Cytoplasmic male sterility (CMS), a typically maternally inherited trait, causes a failure in producing functional pollen. Although the radish CMS has be widely used to produce hybrid varieties in breeding program, the molecular mechanism of CMS in radish is poorly understood. In this study, two radish CMS lines (HYBP-A and YH-A) and their corresponding maintainer lines (HYBP-B and YH-B) were used to identify genes potentially involving in CMS using Illumina pair-end sequencing. A total of 167.86 million clean sequence reads were generated from the eight libraries (two replicates for each line). These reads were eventually assembled into 130,240 unigenes. Of them, 67,173 (51.6%) unigenes were annotated for their function. Comparison of gene expression levels between CMS line and maintainer line revealed 5,893 differentially expressed genes (DEGs) in HYBP, and 3,739 DEGs inYH. There were 990 DEGs commonly identified in both HYBP and YH, with same direction of expression change in two CMS lines relative to their corresponding maintainer lines, which suggested these 990 DEGs is likely related to CMS of radish. The expression levels of 20 DEGs were further confirmed by real-time quantitative PCR (qRT-PCR). Two pathways and eight functional categories exhibited a significant enrichment with DEGs in HYBP, and one pathway and six functional categories were markedly enriched by DEGs in YH. Among these pathways/functional categories, four of them were enriched in both varieties. A series of candidate genes and pathways that may contribute to the CMS will be helpful for increasing our understanding for this trait in radish.
2016-01-21 | GSE65142 | GEO
Project description:high throughput sequencing of the metagenome of mexican children
2020-03-16 | GSE143207 | GEO
Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.
2014-07-20 | GSE48199 | GEO
Project description:In this study, scientific efforts to grasp molecular details underlying vernalization-triggered floral transition were undertaken in radish (Raphanus sativus L.). We performed a comparative transcriptomic analysis between normal flowering ‘Jinjudaepyung’ and very late flowering inbred line, ‘Simu’.
2023-11-01 | GSE239735 | GEO