Chlamydomonas reinhardtii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA264777 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1622080.fastq.gz | Fastqsanger.gz | |||
| SRR1622090.fastq.gz | Fastqsanger.gz | |||
| SRR1622081.fastq.gz | Fastqsanger.gz | |||
| SRR1622091.fastq.gz | Fastqsanger.gz | |||
| SRR1622082.fastq.gz | Fastqsanger.gz |
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Project description:Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications.
2014-10-25 | GSE62671 | GEO
Project description:Biological rhythms in response to both endogenous (circadian) and exogenous (e.g. diel) cycles, with a period of ~24 hours, are a prominent feature of many living systems. In green algal species, knowledge on the extent of diel rhythmicity of genome wide gene expression, its evolution, and its cis-regulatory mechanism is limited. In this study, we identified cyclically expressed genes under diel conditions in Chlamydomonas reinhardtii and found that ~50% of the 17,114 annotated genes exhibited cyclic expression. The cyclic expression patterns indicate a clear succession of biological processes during the course of a day. Among 237 functional categories enriched in cyclically expressed genes, >90% were phase-specific, including photosynthesis, cell division and motility processes. By contrasting cyclic expression between C. reinhardtii and Arabidopsis thaliana putative orthologs, we found significant but weak conservation in cyclic gene expression patterns. On the other hand, within C. reinhardtii cyclic expression was preferentially maintained, particularly amongst older duplicates, and the evolution of phase between paralogs is limited to relatively minor shifts in time. Finally, to better understand the cis regulatory basis of diel expression, putative cis-regulatory elements were identified that could predict the expression phase of a subset of the cyclic transcriptome. Our findings demonstrate both the prevalence of as well as the complex regulatory circuitry required to control cyclic expression in a green algal model, highlighting the need to consider diel expression in studying algal molecular networks and in future biotechnological applications. Total RNA sequences extracted every 3 hours between ZT (Zeitgeber Time, hours since last doawn) 0 and ZT21 from two biological replicates of C. reinhardtiis dw15.1
2014-10-25 | E-GEOD-62671 | biostudies-arrayexpress
Project description:RNA populations in Chlamydomonas reinhardtii Keywords: Highly parallel pyrosequencing
2007-05-16 | GSE7308 | GEO
Project description:Chlamydomonas reinhardtii exposed to various concentrations of silver
2013-10-01 | GSE48677 | GEO
Project description:RNA populations in Chlamydomonas reinhardtii Keywords: Highly parallel pyrosequencing Small RNAs were prepared from Chlamydomonas reinhardtii total extracts,ligated to a 3' adaptor and a 5' acceptor sequentially, and then RT-PCR amplified. PCR products were reamplified using a pair of 454 cloning primers and provided to 454 Life Sciences (Branford, CT) for sequencing. For technical details, see Tao Zhao, Guanglin Li, Shijun Mi, Shan Li, Gregory J. Hannon, Xiu-Jie Wang, and Yijun Qi. 2007. A Complex System of Small RNAs in the Unicellular Green Alga Chlamydomonas reinhardtii. Genes & Development
2007-05-15 | E-GEOD-7308 | biostudies-arrayexpress
Project description:The metabolites derived from microalgae have been attributed with various nutritional and medicinal properties. Therefore, our study aimed to investigate the potential beneficial effects of Chlamydomonas reinhardtii (red), a type of microalgae, in individuals with type 2 diabetes mellitus (T2DM). Mice were fed on high-fat diet and injected with a low dose of streptozotocin to induce T2DM. The diabetic mice were orally treated with either 1% sodium carboxymethylcellulose or Chlamydomonas reinhardtii (red) at doses of 1, 2, or 3 g/kg BW/day for a duration of 4 weeks. The liver sections were subjected to hematoxylin and eosin staining as well as oil red staining for the detection of pathological changes and lipid deposition, respectively. Inflammatory factors in serum were quantified using ELISA kits, while commercial kits were employed to assess oxidative stress-related indicators. Gene expression in liver was analysed by RNA-seq. The results revealed that Chlamydomonas reinhardtii (red) significantly ameliorated fasting blood glucose levels, body weight, triglyceride, and low density lipoprotein cholesterin, while also enhancing oral glucose tolerance and insulin sensitivity. In pathological analysis, Chlamydomonas reinhardtii (red) significantly improved lipid deposition and hepatic tissue damage. Furthermore, Chlamydomonas reinhardtii (red) could obviously decreased the protein expression of G-6-Pase and PEPCK, and regulated the SOCS2/JAK2/STAT5 signaling pathway. Transcriptomic analysis indicated that a total of 972 significantly differentially expressed genes in diabetic mice treated with Chlamydomonas reinhardtii (red). KEGG analyses revealed that lipid and atherosclerosis, MAPK signaling pathway, B cell receptor signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway were involved in Chlamydomonas reinhardtii (red) modulated process. Therefore, the continuous consumption of Chlamydomonas reinhardtii (red) may have anti-T2DM effects through the inhibition of gluconeogenesis, thus offering a promising alternative for T2DM patient.
2025-01-31 | GSE287670 | GEO
Project description:Chlamydomonas reinhardtii exposed to various concentrations of silver For this experiment,C. reinhardtii were exposed to (4) different concentrations of silver, as biological triplicates
2013-10-01 | E-GEOD-48677 | biostudies-arrayexpress
Project description:endogenous small RNAs from Chlamydomonas reinhardtii strain J3(mt-) vegetative cells Keywords: High throughput 454 small RNA sequencing
2007-06-04 | GSE7575 | GEO
Project description:Agilent gene expression microarrays (Bham Chlamydomonas reinhardtii Agilent-029192 15k v1) were used to profile transcriptional changes afeter exposure of Chlamydomonas reinardtii algae to cerium dioxide nanoparticles.
2014-09-01 | E-MTAB-2454 | biostudies-arrayexpress
Project description:We analysed global gene expression changes in Chlamydomonas reinhardtii in response to 1h UV-B, applied at the same low level that was seen to promote subsequent UV-B stress tolerance, in order to elucidate the transcriptional reprogramming that leads to UV-B acclimation. mRNA profiles generated by deep sequencing from triplicate replicate Chlamydomonas reinhardtii samples sourced from independent cultures either protected from UV-B or exposed to 1h acclimation-level UV-B.
2015-11-11 | E-GEOD-68739 | biostudies-arrayexpress