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ABSTRACT:
PROVIDER: PRJNA391092 | ENA |
REPOSITORIES: ENA
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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: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:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae. Identification of blue light and red light regulated genes by deep sequencing in biological duplicates. qRT-PCR was performed to verify the RNA-seq results.
2016-09-01 | E-GEOD-67303 | biostudies-arrayexpress
Project description:Animal pigment patterns play important roles in behavior and, in many species, red coloration serves as an honest signal of individual quality in mate choice. Among Danio fishes, some species develop erythrophores, pigment cells that contain red ketocarotenoids, whereas other species, like zebrafish (D. rerio) only have yellow xanthophores. Here, we use pearl danio (D. albolineatus) to assess the developmental origin of erythrophores and their mechanisms of differentiation. We show that erythrophores in the fin of D. albolineatus share a common progenitor with xanthophores and maintain plasticity in cell fate even after differentiation. We further identify the predominant ketocarotenoids that confer red coloration to erythrophores and use reverse genetics to pinpoint genes required for the differentiation and maintenance of these cells. Our analyses are a first step towards defining the mechanisms underlying the development of erythrophore-mediated red coloration in Danio and reveal striking parallels with the mechanism of red coloration in birds.
2021-05-20 | GSE174713 | GEO
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:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
2016-09-01 | GSE67303 | GEO
Project description:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
2016-09-10 | GSE83828 | GEO
Project description:<p>Shrub willow has strong adaptability, large biomass and short rotation period. Colorful willow barks have great ornamental and economic value. To study the color regulation mechanism, metabolomics and transcriptomics were used to analyze the purple, green and red barks. In the positive mode, a total of 1639 metabolites were identified and 1026 metabolites in negative mode. Flavone and flavonol biosynthesis (ko00944), flavonoid biosynthesis (ko00941), were all enriched in the 3 groups G vs P (G/P), G vs R (G/R) and P vs R (P/R). A total of 12 flavone and flavonol biosynthesis metabolites were isolated. A total of 448,839,796 raw reads were obtained with Q30 more than 93.15%. In the G/P, G/R and P/R groups, 27, 28 and 21 genes were enriched in the flavonoid biosynthesis (ko00941). The expression of CHS, ANS, DFR, ANR in the flavonoid biosynthesis pathway was the most in red. The content of canthaxanthin in purple bark was 10x more than green and 6x than red. The integration of metabolites and genes indicated the role of pelargonidin and canthaxanthin in regulating red and purple color pigment. Our research provides a fundamental basis for colorful willow breeding.</p>
2022-08-10 | MTBLS4820 | MetaboLights
Project description:RNA-seq was used in combination with various analytical chemistry approaches to identify the chemical and genetic basis of pigment production of the bacterium Glutamicibacter arilaitensis when growing on cheese. This bacterium commonly found in cheese rinds where it co-occurs with Penicillium species and other molds. Pinkish-red pigments are produced by the bacterium in response to growth with Penicillium. Both chemical analyses and RNA-seq point to coproporphyrin III as the major metabolite leading to pigment formation.
2018-04-01 | GSE112092 | GEO