Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA377137 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genes significantly down or Up-regulated upon RNF219 knockdown
| PRJNA377128 | ENA
Project description:In this study, we analyzed the function of RNF219 in gene expression control by RNA-Seq analyses in mouse embryonic stem cells after RNF219 knockdown.
2021-03-05 | GSE146511 | GEO
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:We knocked down the lncRNA-Neat1 by RNA interference in HT22 cells, which were immortalized from the mice hippocampal neurons. Then we measured the mRNA alteration induced by Neat1 knockdown through the next generation sequencing technique (RNA-seq). A total of 18,309 transcripts were detected in the current sequencing study, in which 593 transcripts were selected out according to the criteria: |log2(fold change)| > 1, P < 0.05 (22 up-regulated and 571 down-regulated). To explore whether the mRNA change induced by Neat1 knockdown in a stressed culture condition was different from that in normal condition, the cells were dealt with OGD and followed by RNA-seq. A total of 18,502 transcripts were detected, in which 121 transcripts were significantly up-regulated and 126 transcripts were significantly down-regulated according to the aforementioned filter rules.
2019-08-17 | GSE85749 | GEO
Project description:For analysis of genes regulated by HP1γ in LUAD, we used microarray analysis to determine the global changes in gene expression upon HP1γ knockdown in H1792 cells and identified distinct sets of up-regulated and down-regulated genes upon depletion of HP1γ.
2018-11-13 | GSE111321 | GEO
Project description:Over the past decades, Helicoverpa armigera nucleopolyhedrovirus (HearNPV) has been widely used for biocontrol of cotton bollworm, which is one of the most destructive pest insects in agriculture worldwide. However, the molecular mechanism underlying the interaction between HearNPV and host insects remains poorly understood. In this study, high throughput RNA-sequencing was integrated with label-free quantitative proteomics analysis to examine the dynamics of gene expression in the fat body of H. armigera larvae in response to challenge with HearNPV. RNA-sequencing-based transcriptomic analysis indicated that host gene expression was substantially altered, yielding 3,850 differentially expressed genes (DEGs), while no global transcriptional shut-off effects were observed in the fat body. Among the DEGs, 60 immunity-related genes were down-regulated after baculovirus infection, a finding that was consistent with the results of quantitative real-time RT-PCR (qRT-PCR). Gene ontology and functional classification demonstrated that the majority of down-regulated genes were enriched in gene cohorts involved in energy, carbohydrate, and amino acid metabolic pathways. Proteomics analysis identified differentially expressed proteins in the fat body, among which 76 were up-regulated, whereas 373 were significantly down-regulated upon infection. The down-regulated proteins are involved in metabolic pathways such as energy metabolism, carbohydrate metabolism (CM), and amino acid metabolism, in agreement with the RNA-seq data. Furthermore, correlation analysis suggested a strong association between the mRNA level and protein abundance in the H. armigera fat body. More importantly, the predicted gene interaction network indicated that a large subset of metabolic networks was significantly negatively regulated by viral infection, including CM-related enzymes such as aldolase, enolase, malate dehydrogenase and triose-phosphate isomerase. Taken together, transcriptomic combined with proteomic data elucidated that baculovirus established systemic infection of host larvae, and manipulated the host mainly by suppressing the host immune response and down-regulating metabolism to allow viral self-replication and proliferation. Therefore, this study provided important insights into the mechanism of host-baculovirus interaction.
2017-04-19 | PXD004748 | Pride
Project description:Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to find out the difference between SYK stable knockdown and negative control group in each cancer cell line, and find the transcriptomes change upon SYK knockdown. Methods: mRNA profiles of cell lines were generated using Illumina PE150, then GSEA was used for analyzing the association between SYK knockdown and the mesenchymal or epithelial signature. Results: The result showed epithelial signatures were up-regulated, while mesenchymal signatures were down-regulated upon SYK knockdown in RNA-seq data. Conclusions: Our study systematically examined the cellular transcriptomes affected by SYK knockdown, with biologic replicates, generated by RNA-seq technology. SYK knockdown results in the transcriptional change of multiple epithelial and mesenchymal markers, leading to mesenchymal state switching.
2023-05-24 | GSE125956 | GEO
Project description:The evolutionarily conserved CCR4-NOT complex acts as a central player in the control of mRNA turnover and mediates accelerated mRNA degradation upon histone deacetylase (HDAC) inhibition. Here, we explored acetylation-induced changes in the composition of the CCR4-NOT complex by purification of the endogenously tagged scaffold subunit NOT1 and identified ring finger protein 219 (RNF219) as an acetylation-regulated cofactor. We provide evidence that RNF219 is an active RING-type E3 ubiquitin ligase which stably associates with the CCR4-NOT complex via the NOT9 module through a short linear motif located in the C-terminal low-complexity region of RNF219. Using a reconstituted six-subunit human CCR4-NOT complex, we demonstrate that RNF219 acts as an inhibitor of deadenylation. Accordingly, our transcriptome-wide mRNA half-life measurements reveal that RNF219 attenuates global mRNA turnover in cells, independently of its E3 ligase activity. Our results establish RNF219 as a negative regulator of CCR4-NOT-mediated mRNA deadenylation, whose loss upon HDAC inhibition contributes to accelerated mRNA turnover.
2021-10-27 | GSE172019 | GEO
Project description:We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3â??-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, HMGB1, KLF12 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of HMGB1, KLF12 and CIT was detected in advanced stages of cancer. This study provides new insights and a comprehensive catalogue of p53-mediated regulations and p53 DNA binding in CRC cells.
2016-05-24 | MSV000079767 | MassIVE
Project description:We performed RNA sequencing (RNA-Seq) based transcriptomic profiling of aortae from C57BL/6 mice by control or 24-hr fasting. Our RNA-Seq analysis revealed 529 altered genes (1.5 fold change, p<0.05), of which 278 genes were significantly up-regualted and 251 genes were significantly down-regulated in aortae isolated from mice by 24-hr fasting.Gene ontology and pathway analysis of the up-regulated genes indicated that multiple biological processes were enriched including regulation_of_cellular_metabolic_process, while the down-regulated genes were enriched in the biological processes such as sterol_biosynthetic_process.
2024-01-24 | GSE173564 | GEO