ScRNA-seq of male mouse aorta collected over the light-dark cycle
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ABSTRACT:
PROVIDER: PRJNA851414 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19768936.fastq.gz | Fastqsanger.gz | |||
| SRR19768937.fastq.gz | Fastqsanger.gz | |||
| SRR19768938.fastq.gz | Fastqsanger.gz | |||
| SRR19768939.fastq.gz | Fastqsanger.gz | |||
| SRR19768940.fastq.gz | Fastqsanger.gz |
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Project description:scRNA-seq of male mouse aorta collected over the light-dark cycle
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Project description:Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis.
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Project description:We investigated the transcriptional response of cand. Pelagibacter ubique cultures to light and dark when grown under carbon replete and deplete conditions. Results: During exponential phase, few genes were differentially transcribed between light:dark growth conditions. In stationary phase, a high proportion (9.7%) of coding sequences were found differentially expressed between treatments; 4.7% being up-regulated in the light (n=64) and 4.9% being up-regulated in the dark (n=67). Several components of the oxidative phosphorylation pathway were up-regulated in the dark, supporting physiological data showing higher respiration rates in darkness than in the light under starvation conditions. We also observed up-regulation of a proton translocating pyrophosphate synthase (SAR11_1040), which may be an additional energy production mechanism utilized by SAR11 cells in the dark. Finally, we noted the up-regulation of pili formation genes in the array data, consistent with the observation of pili in dark grown cells via electron microscopy.
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Project description:Mice are on a C57Bl/6N background strain, hearts were collected at ZT07, following 4 weeks under a 12h light: 12h dark (LD) or 12h light: 4h blue: 8h dark (LBD) cycle. The microarray approach allows the investigation of gene expression changes of all genes in WT LD vs. WT LBD hearts.
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Project description:Investigation of whole genome gene expression level changes in Trichodesmium erythraeum IMS101 during a 24-hr light and dark cycle. The diel gene expression analyzed in this study is further described in Muñoz-Marin, M., I. N. Shilova, T. Shi, H. Farnelid & J. P. Zehr. 2019. The transcriptional cycle is suited to daytime N2 fixation in the unicellular cyanobacterium “Candidatus Atelocyanobacterium thalassa” (UCYN-A). mBio 10:e02495-18. https://doi.org/10.1128/mBio.02495-18.
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Project description:Nannochloropsis oceanica CCMP1779 is a marine unicellular stramenopile and an emerging reference species for basic research on oleogenic microalgae with biotechnological relevance. We investigated its physiology and transcriptome under light/dark cycles. We observed oscillations in lipid content and a predominance of cell division in the first half of the dark phase. Globally, more than 60% of the genes cycled in N. oceanica CCMP1779, with gene expression peaking at different times of the day. Interestingly, the phase of expression of genes involved in certain biological processes was conserved across photosynthetic lineages. Furthermore, in agreement with our physiological studies we found the processes of lipid metabolism and cell division enriched in cycling genes. For example, there was tight coordination of genes involved in the lower part of glycolysis, fatty acid synthesis and lipid production at dawn preceding lipid accumulation during the day. Our results suggest that diel lipid storage plays a key role for N. oceanica CCMP1779 growth under natural conditions making this alga a promising model to gain a basic mechanistic understanding of triacylglycerol production in photosynthetic cells. Our data will help the formulation of new hypotheses on the regulation transcriptional control of cell growth and metabolism in Nannochloropsis. Nannochloropsis oceanica CCMP was entrained to 12:12 light:dark cycles and biological replicates collected every 3 hours for a cycle for a total of 16 samples.
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Project description:We investigated differences in gene expression in left ventricular tissue from WT and ΔKPQ (Scn5aΔ/+) mice. Tissue was collected diurnally at the phase transitions from dark to light (D:L) and light to dark (L:D). We employed RNAseq (Novogene) to examine potential variances between the two strains of mice, as well as, any differences in expression at the two time points. RNAseq provided a snapshot of gene expression which revealed an intact molecular clock for both strains. Previous studies have demonstrated circadian peak or trough at the light phase changes in cardiac tissue in mice for many core molecular clock components. Similar to these studies both strains demonstrated a significant difference in expression between core molecular clock genes Bmal1, Clock, Per1, Per2, Per3 assessed at the phase transitions. This assessment revealed 39 diurnally expressed genes. To our surprise, only 6 genes were differently expressed between the two strains of mice.
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