Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11106900_1.fastq.gz | Fastqsanger.gz | |||
| SRR11106900_2.fastq.gz | Fastqsanger.gz | |||
| SRR11106901_1.fastq.gz | Fastqsanger.gz | |||
| SRR11106901_2.fastq.gz | Fastqsanger.gz | |||
| SRR11106902_1.fastq.gz | Fastqsanger.gz |
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Project description:Bacillus velezensis strain GH1-13 isolated from a rice paddy soil in Korea has been reported to promote plant growth and inhibit some pathogens. It contains a plasmid pBV71, thought to be of benefit to the strain, but there is no information on its effect. In order to elicit the plasmid effect on gene expression, mRNA and protein levels were analyzed at various stages of bacterial growth. Comparative gene expression profiles between the plasmid-containing and plasmid-free cells revealed that strain GH1-13 activated a transient stress response in the exponential phase. It showed early activation of expression of sigma W operon, liaIHGFSR operon, and transcription regulators for transition state, associated with carbon catabolite repression and secondary metabolite biosynthesis of acetoin, bacillaene, and macrolactin.
2021-05-17 | PXD008573 | Pride
Project description:Pituitary gland function is regulated by the activity of various transcription factors which control cell fate decisions leading to cellular differentiation and hormone production. FOXO1 is necessary for the proper timing of somatotrope differentiation and for somatotrope function, but the exact mechanism of action has yet to be elucidated. Recent data implicate FOXO1 in the regulation of genes important for somatotrope differentiation including Gh1, Neurod4, and Pou1f1. Previously, a mouse model with conditional deletion of Foxo1 from the developing pituitary gland displayed reduced Gh1 and Neurod4 transcripts as early as embryonic day 18.5. Additional data from adult animals with conditional deletion of both Foxo1 and Foxo3 from the pituitary gland have a similar reduction in Neurod4 and Gh1, as well as Pou1f1. To investigate the mechanism by which FOXO1 regulates pituitary gland gene expression and confirm in vivo findings, the somatotrope-like cell line, GH3, was treated with the FOXO1 inhibitor, AS1842856, for 24 hours at various concentrations. Neurod4 was the most severely affected genes with a dose-dependent reduction in transcript at inhibitor concentrations as low as 30 nM. Gh1 transcripts were significantly reduced at 300 nM. Pou1f1 expression was trending down at 3 microM inhibitor (p=0.066). Consistent with these findings, CRISPR/Cas9-mediated deletion of Foxo1 in GH3 cells significantly reduced expression of Gh1, Neurod4, but not Pou1f1. To elucidate the molecular mechanisms underlying the role of FOXO1 in somatotropes, ChIPseq was performed for FOXO1 in the GH3 cell line. This study identified novel FOXO1 binding sites associated with the Neurod4, Gh1, and Pou1f1 genes. The FOXO1 binding site in the Neurod4 gene exhibits enhancer activity in somatotrope-like cells, but not in gonadotrope-like or heterologous cells. These data strongly suggest FOXO1 directly contributes to the transcriptional control of genes important for somatotrope differentiation. These novel findings contribute to the much-needed understanding of pituitary cell fate decisions.
2023-12-14 | GSE245740 | GEO
Project description:The depressive-like behavior in animals is usually assessed by standardized behavioral tests such as the forced swimming test. However, the findings of these tests may be affected by individual variability among animals, which may hinder the discovery of genes responsible for depression. Few reports have showed the influence of individual variability in identifying the genes associated with depressive-like behavior. In this study, we measured the immobility ratio (% immobility in 5 min) in the forced swimming test in 106 male Wistar rats. According to the distribution of individual immobility ratio, the rats were divided into three groups: the control group with immobility ratio -1 to +1 standard deviation (SD) from the mean, the depressive group with immobility ratio +1 to +2 SD above the mean, and the anti-depressive group with immobility ratio -1 to -2 SD below the mean. Microarray analysis was used to identify the genes differentially expressed by depressive group rats in the prefrontal cortex and cerebellum. The differentially expressed genes in both brain regions of the depressive group were Alas2, Gh1, Hba-a2, Hbb, Hbb-b1, Hbe2, LOC689064, Mrps10, Mybpc, Olf6415, and Pfkb1. Ingenuity pathway analysis identified Gh1 as a hub gene in the networks of the differentially expressed genes in both brain regions. This study indicates that inherent differences in depressive-like behavior may be related to the Gh1 expression in the cerebellum and prefrontal cortex. We measured the immobility ratio of 106 normal rats using the forced swimming test and statistically analysis. We selected the rats exhibitting depressive-like behavior or average in the 106 rats. Total RNA was prepareted from the cerebellum and prefrontal cortex. An equal amount of RNA from 4 rats in each group was pooled and used for microarray analysis.
2015-02-26 | E-GEOD-63377 | biostudies-arrayexpress
Project description:Chromatin architecture relies on histone H1 whose central globular domain (GH1) sits on the nucleosome dyad and carboxy-terminal domain associates with linker DNA. We report that Arabidopsis H1 positively influences H3K27me3 chromatin enrichment over protein-coding genes but oppositely prevents its accumulation on telomeres and heterochromatic Interstitial Telomeric Repeats (ITRs). Contrasting with their neighboring heterochromatic environment, pericentromeric ITR regions remain highly compacted and are more prone to long-distance interactions with telomeres in H1 mutant plants. The switch from H1-rich to H3K27me3-rich ITR chromatin is further accompanied by an invasion of GH1-Myb Telomeric Repeat Binding protein 1 (TRB1), a structural component of telomeres capable to trigger H3K27me3 deposition over protein-coding genes displaying short telomeric motifs. This dual effect led us to propose a competition mechanism between H1 and TRB that prevents massive H3K27me3 deposition over large blocks of repeated motifs, thereby contributing to regulate H3K27me3 homeostasis over the genome.
2023-09-10 | GSE190825 | GEO
Project description:Chromatin architecture relies on histone H1 whose central globular domain (GH1) sits on the nucleosome dyad and carboxy-terminal domain associates with linker DNA. We report that Arabidopsis H1 positively influences H3K27me3 chromatin enrichment over protein-coding genes but oppositely prevents its accumulation on telomeres and heterochromatic Interstitial Telomeric Repeats (ITRs). Contrasting with their neighboring heterochromatic environment, pericentromeric ITR regions remain highly compacted and are more prone to long-distance interactions with telomeres in H1 mutant plants. The switch from H1-rich to H3K27me3-rich ITR chromatin is further accompanied by an invasion of GH1-Myb Telomeric Repeat Binding protein 1 (TRB1), a structural component of telomeres capable to trigger H3K27me3 deposition over protein-coding genes displaying short telomeric motifs. This dual effect led us to propose a competition mechanism between H1 and TRB that prevents massive H3K27me3 deposition over large blocks of repeated motifs, thereby contributing to regulate H3K27me3 homeostasis over the genome.
2023-09-10 | GSE160411 | GEO
Project description:Chromatin architecture relies on histone H1 whose central globular domain (GH1) sits on the nucleosome dyad and carboxy-terminal domain associates with linker DNA. We report that Arabidopsis H1 positively influences H3K27me3 chromatin enrichment over protein-coding genes but oppositely prevents its accumulation on telomeres and heterochromatic Interstitial Telomeric Repeats (ITRs). Contrasting with their neighboring heterochromatic environment, pericentromeric ITR regions remain highly compacted and are more prone to long-distance interactions with telomeres in H1 mutant plants. The switch from H1-rich to H3K27me3-rich ITR chromatin is further accompanied by an invasion of GH1-Myb Telomeric Repeat Binding protein 1 (TRB1), a structural component of telomeres capable to trigger H3K27me3 deposition over protein-coding genes displaying short telomeric motifs. This dual effect led us to propose a competition mechanism between H1 and TRB that prevents massive H3K27me3 deposition over large blocks of repeated motifs, thereby contributing to regulate H3K27me3 homeostasis over the genome.
2023-09-10 | GSE160408 | GEO
Project description:Chromatin architecture relies on histone H1 whose central globular domain (GH1) sits on the nucleosome dyad and carboxy-terminal domain associates with linker DNA. We report that Arabidopsis H1 positively influences H3K27me3 chromatin enrichment over protein-coding genes but oppositely prevents its accumulation on telomeres and heterochromatic Interstitial Telomeric Repeats (ITRs). Contrasting with their neighboring heterochromatic environment, pericentromeric ITR regions remain highly compacted and are more prone to long-distance interactions with telomeres in H1 mutant plants. The switch from H1-rich to H3K27me3-rich ITR chromatin is further accompanied by an invasion of GH1-Myb Telomeric Repeat Binding protein 1 (TRB1), a structural component of telomeres capable to trigger H3K27me3 deposition over protein-coding genes displaying short telomeric motifs. This dual effect led us to propose a competition mechanism between H1 and TRB that prevents massive H3K27me3 deposition over large blocks of repeated motifs, thereby contributing to regulate H3K27me3 homeostasis over the genome.
2023-09-10 | GSE160410 | GEO
Project description:Bacillus velezensis strain GH1-13 with a native conjugative plasmid (pBV71) is thought to be beneficial to the bacterium, although no information on its effects exists. Here we show that strain GH1-13 frequently lost the plasmid during normal growth conditions in a rich medium and changed the morphology and sensitivity to selenite and tellurite. Compared to the plasmid-cured cells, the wild-type and complemented cells exhibited multicellular behavior with the expression of conjugative type IV pili and regulatory Rap homologous genes that regulate the interconnection between conjugation and biofilm formation. Further omics-based analyses of morphogenesis, biofilm formation, and antibiotic synthesis suggest that the conjugative plasmid activates envelope stress responses in association with increased biosynthesis of extracellular polysaccharide and antibiotics for protective functions of the host during exponential phase.
2021-05-17 | PXD017305 | Pride
Project description:Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. cerevisiae relative to the transporter with Neurospora-derived coding sequence (hereafter NC for the mRNA). We performed ribosome profiling and RNA deep sequencing of cells expressing NC and OPT grown at mid-exponential phases, respectively. Differences in ribosome occupancy on NC and OPT transcripts suggested increased rates of translation elongation of the N-terminal sequence of OPT in contrast to NC, which may be responsible for the slow-growth phenotype of cells expressing OPT.
2018-06-30 | GSE75004 | GEO