Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE264674 | GEO | 2024/05/29
REPOSITORIES: GEO
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Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.
2021-04-19 | GSE163128 | GEO
Project description:There had a total number of 804 genes with transcript difference, including 482 up-regulated genes and 322 down-regulated genes. Enrichment analysis of those 804 different transcript gene sets was performed to explore the biological effects and the corresponding pathways that are significantly associated on GO and KEGG (Padj <0.05 as the threshold for significant enrichment). In the GO functional enrichment analysis, all differential genes were significantly enriched into 65 GO Terms, among them there had 50 GO terms belonging to BP (Biological Process). Among these BP 50 terms, organonitrogen compound metabolic process (44 genes), organonitrogen compound biosynthetic process (44 genes), and oxidation-reduction process (58 genes) had most different transcript gene sets. While in the MF (Molecular Function), there had 3 GO terms involved transcript changes, which including coenzyme binding (31 genes), structural constituent of ribosome (17 genes) and structural molecule activity (17 genes). In the KEGG pathways enrichment analysis, all differential genes were significantly enriched mainly into 4 pathways, including efq03010 (Ribosome, 30 genes), efq01212 (Fatty acid metabolism, 10 genes), efq00061 (Fatty acid biosynthesis, 10 genes), and efq02010 (ABC transporters, 19 genes), where efq03010 (Ribosome), efq01212 (Fatty acid metabolism), efq00061 (Fatty acid biosynthesis) were up-transcripted pathways, and efq02010 (ABC transporters) was the down-transcripted pathway. Based on transcriptome data analysis in selenium-enriched E. durans A8-1 compared with E. durans A8-1, a total of 19 genes were screened for significant up- transcripted that may be associated with selenium metabolic processes
2023-12-01 | GSE188295 | GEO
Project description:To explore the specific functional and cellular processes that affected by the mC10orf71 deletion, we compared total RNA expression in hearts from E18.5. Gene Ontology (GO) enrichment analysis showed that down-regulated genes were not significantly enriched in any biological process. The 327 genes up-regulated in KO mice were enriched for energy generation, electron transport chain and ATP synthesis, and many of them are encoded by mitochondrial DNA. These changes were likely to be a compensatory response to the impaired morphogenesis and dysfunction of the KO hearts. Then, we performed RNA-seq on hearts of adult WT and KO mice. GO analysis of down-regulated genes identified two categories of biological processes: mRNA processing/splicing and muscle cell differentiation/contraction.
2024-06-06 | GSE264733 | GEO
Project description:Intervention type:DRUG
Name of intervention:Huaier
Dose form / Japanese Medical Device Nomenclature:GRANULES
Route of administration / Site of application:ORAL
Dose per administration:20?
g
Dosing frequency / Frequency of use:OTHER, SPECIFY
20g? per day
Planned duration of intervention:3 months to extending if necessary
Intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary
detailes of teratment arms:hepatocellular carcinoma, breast cancer, colorectal cancer and related gastrointestinal cancers, urologic cancers including prostate cancer, pancreas cancer, and lung cancer, etc.
Comparative intervention name:None
Dose form / Japanese Medical Device Nomenclature:
Route of administration / Site of application:
Dose per administration:
Dosing frequency / Frequency of use:
Planned duration of intervention:
Intended dose regimen:
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.
Study Design: Comparative test, None, No, open(masking not used), EXPLORATORY
| 98681 | ecrin-mdr-crc
Project description:Purpose: Analysis of the regulatory network involved in DSTY in lung cancer cells. Methods: mRNA profiles of A549 knockdown cell group and A549 NC group were generated by deep sequencing, using Illumina Novaseq platform. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed. Clusterprofiler software was used to perform GO function enrichment analysis and KEGG pathway enrichment analysis of the differential gene sets. Results: We identified 2555 differential genes, of which 1444 were up-regulated and 1111 were down-regulated in A549 sh1 VS NC. In GO enrichment analysis,the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in inflammation response,chemotaxis,innate immune response, and extracellular matrix. KEGG analysis shows that differential genes are enriched in cytokine-cytokine receptor interaction ,JAK-STAT signaling pathway and PI3K-Akt signaling pathways.We identified 2600 differential genes, of which 1523 were up-regulated and 1077 were down-regulated in A549 sh4 VS NC. In GO enrichment analysis,the biological process is mainly in the cell ions homeostasis and the molecular function is mainly in chemokine receptor binding,nic hydroxy compound metabolic process,alcohol metabolic process, and extracellular matrix. KEGG analysis shows that differential genes are enriched in cytokine-cytokine receptor interaction ,glutathione metabolism and chemical carcinogenesis. Conclusion: Based on RNA-seq analysis, the regulatory network involved in DSTY in Lung cancer .
2021-06-19 | GSE178487 | GEO
Project description:In this study, we used RNA-Seq to analyze the transcriptome of BK KO/WT mice hippocampus and cortex, and performed transcriptome profiling to characterize the differentially expressed genes. A total of 652 genes were screened with the threshold of significance at P < 0.05 and |log2foldchange| > 0.58, among which 382 genes were down-regulated and 270 genes were up-regulated in hippocampus tissues. In cortex tissues, we detected a total of 561 differentially expressed genes with the threshold of significance at P < 0.05 and |log2foldchange| > 0.58, including 162 up-regulated genes and 399 down-regulated genes. In order to better understand the potential functions of differentially expressed genes, Gene Ontology (GO) enrichment analysis was carried out to assess the involved pathways. Biological process pathway in GO analysis results showed that development process and biological adhesion were enriched. The results of kyoto encyclopedia of genes and genomes (KEGG) showed that insulin secretion, axon guidance, p53 signaling pathway, HIF-1 signaling pathway and calcium signaling pathway were enriched in hippocampus. On the other hand, cortical KEGG results showed that cell adhesion molecules (CAMs), ECM-receptor interaction, phagosome and calcium signaling pathway were enriched. Dysregulation of gene expression, especially astrocyte activation, neuroinflammation and autophagy, might be the molecular mechanism of BK-LOF meditated epilepsy. This study explores the possible mechanism of epilepsy by transcriptome, reveals the relationship between KCNMA1-LOF and epilepsy, and provides a possible molecular template for individualized treatment of epilepsy.
2021-12-18 | GSE191038 | GEO
Project description:Most significantly affected GOs by TST stress include Cellular localization, transport and migration such as Cellular macromolecule localization (GO:0070727), Intracellular transport (GO:0046907) and Intracellular protein transport (GO:0006886), metabolic processes such as Small molecule metabolic process (GO:0044281), Cellular amide metabolic process (GO:0043603) and Lipid metabolic process (GO:0006629), neuronal cell population differentiation and proliferation such as Neurogenesis (GO:0022008), Neuron differentiation (GO:0030182), Glial cell differentiation (GO:0010001), Central nervous system development (GO:0007417), Astrocyte differentiation (GO:0048708) and Gliogenesis (GO:0042063), and cell signaling such as G-protein-coupled receptor signaling pathway (GO:0007186), Negative regulation of signaling (GO:0023057), Positive regulation of signaling (GO:0023056), Response to endogenous stimulus (GO:0009719) and Regulation of intracellular signal transduction (GO:1902531). Peptide metabolic process (GO:0006518), Peptidyl amino acid modification (GO:0018193), Regulation of steroid biosynthetic process (GO:0050810) were also significantly enriched in the TST stress-induced mice brain. Top significantly enriched Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways by the stress response related DEGs between high-dose RE vs TST include mitogen-activated protein kinase (MAPK) signaling pathway, Chemokine signaling pathway, Neurotrophin signaling pathway, Cytokine-cytokine receptor interaction, GnRH signaling pathway, ErbB signaling pathway, Toll-like receptor signaling pathway, T cell receptor signaling pathway, B cell receptor signaling pathway, vascular endothelial growth factor (VEGF) signaling pathway, Long-term depression, NOD-like receptor signaling pathway, Insulin signaling pathway, Jak-STAT signaling pathway, Apoptosis, and mTOR signaling pathway.
2021-07-29 | GSE180884 | GEO
Project description:To understand molecular pathogenesis of chemical induced contact dermatitis, cultured normal human epidermal keratinocytes (NHKCs) were treated with sub-cytotoxic concentration of sodium lauryl sulfate (SLS, 10 microM) and urushiol (1 microM). In analysis, 259 genes were selected as up-regulated DEGs in the SLS-treated NHKCs and 193 genes as down-regulated DEGs. In urushiol-treated NHKCs, 173 up-regulated and 124 down-regulated DEGs were identified. Gene Ontology (GO) biological process (BP) in the SLS-induced upregulated DEGS in NHKCs were inflammation-associated biological processes, such as inflammatory response (GO:0006954), cellular response to calcium ion (GO:0071277), immune response (GO:0006955) and cellular response to lipopolysaccharide (GO:0071222) and in urushiol-induced upregulated DEGs were inflammation-associated biological processes such as cytokine-mediated signaling pathway (GO:0019221) and inflammatory response (GO:0006954). SLS downregulated proteins in chemotaxis (GO:0006935), oxidation-reduction process (GO:0055114), cornification (GO:0070268), G1/S transition of mitotic cell cycle (GO:0000082), keratinization (GO:0031424) and cellular protein metabolic process (GO:0044267) and urushiol downregulated proteins in nervous system development (GO:0007399), positive regulation of cell proliferation (GO:0008284) and cellular protein metabolic process (GO:0044267) significantly.
2019-11-01 | GSE126354 | GEO
Project description:Non-alcoholic steatohepatitis (NASH), has emerged as a major cause of liver failure and hepatocellular carcinoma. Although decades of studies have improved our understanding of its pathophysiology, the molecular mechanisms are still incompletely understood. In the current study, using a diet-induced mouse model of NASH, we performed RNA Sequencing analysis to reveal molecular features of NASH progression. As a result, we obtained hepatic genome-wide mRNA expression in the livers from two groups of mice (NASH versus Normal).Using FDR < 0.01 and fold change > 2 as the threshold, we identified 1745 differentially expressed genes (DEGs) in the livers of NASH mice relative to the normal control mice, of which 1484 up-regulated and 261 down-regulated. The top 5 up-regulated genes included the genes encoding for Trem2, Lcn2, Ephb2, Mmp12 and Sprr1a.Gene ontology (GO) analysis showed that the up-regulated genes in NASH mice were mainly enriched in biological processes such as response to biotic stimulus, regulation of immune system process and myeloid leukocyte activation, while down-regulated genes were related to organonitrogen compound biosynthetic process and organic acid metabolic process.KEGG pathway enrichment results showed that up-regulated genes were mainly enriched in toll like receptor signaling, regulation of actin cytoskeleton, leukocyte transendothelial migration, chemokine signal pathway as well as cytokine and cytokine receptor interaction, while down-regulated gene clusters were mainly enriched in and steroid biosynthetic as well as glycine serine and threonine metabolism.Meanwhile, as expected, genes involved in hepatic lipogenesis (Srebp-1c, Fasn and Scd-1), lipid absorption (CD36), inflammation (Tnfa, IL1b and Ccl2), and fibrosis (Col1a1, Tgfb1 and Mmp13), are up-regulated in NASH mice.Our study may help to uncover NASH molecular basis and provide therapeutic targets for its treatment.
2021-11-20 | GSE189066 | GEO