Exploring the underlying mechanism by which circHNRNPU_603aa exerted carcinogenesis and its potential targets in MM
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE174501 | GEO | 2022/03/15
REPOSITORIES: GEO
Similar Datasets
Project description:Control CAG-GFP or CAG-Zfp292 (Zfp292-OE) plasmids were electroporated into P0 mouse pups in vivo. We harvested the retinas 4 days later to allow for robust expression, dissociated the retinas into single cell preps, collected the GFP+ Retinal progenitor cells (RPCs) via FACS sorting from control or Zfp292-OE conditions, and processed the cells for bulk RNA-seq.
2023-05-31 | GSE229872 | GEO
Project description:To identify ZNF506 genome-wide target sites, we performed ChIP-seq assay and found that ZNF506 binding sites enriched at PBS-Pro-containing ERV subfamilies (ERVPs) and further motif calling analysis showed that ZNF506 binds to PBS-Pro sequences, promoting formation of H3K9me3 modifications at binding regions. And ChIP-seq assay also indicated that the distinction of H3K9me3 signals closed to ZNF506 peak regions between ZNF506 overexpressing (OE) HEK293T cells and ZNF506 Knockout (KO) HEK293T cells was correlated with the different recruitment of corepressor KAP1. The ChIP-seq experiments using GFP antibodies and H3K9me3 antibodies on ZNF506-GFP OE HEK293T cell lines, and ZNF417-GFP OE HEK293T cell lines were used as controls for H3K9me3 ChIP. Also, the ChIP-seq experiments were performed using H3K9me3 antibodies and KAP1 antibodies on ZNF506 KO HEK293T cells and ZNF506 OE HEK293T cells.
2023-07-26 | GSE209826 | GEO
Project description:To verify genes that are directly regulated by BysR, we used DNA affinity purification sequencing analysis (DAP-seq) for genome-wide recognition of BysR binding sites in vitro. The HALO-fusion BysR protein was successfully expressed and purified. After affinity purification and sequencing, at least 22 million double-end reads per sample were generated and with > 99 % of reads uniquely mapped to the JP2-270 genome. A total of 470 enriched common peaks of two replicates with –log10(P-value) ≥ 2 were called . The mean width of DAP-seq peaks was < 1,000. In total, 367 (78%) of these peaks were found to locate in the -1 kbp to 1 kbp regions by the analysis of peak summit positions relative to the start codons of JP2-270 open reading frames.
2022-11-22 | GSE193916 | GEO
Project description:Mesembryanthemum crystallinum (common ice plant) is one of the most important halophyte plants for plant stress biology research. In this study, we established an efficient Agrobacterium-mediated transformation method in ice plant and confirmed that ice plant can sustain gene overexpression for four weeks. Expression of a salt-induced transcription factor McHB7 (OE) reached the highest level at seven days after infiltration. Under salt and drought stresses, the growth of OE was better than wild type (WT), and the activities of redox enzymes and chlorophyll contents were higher in OE than the WT. Using proteomics, 475, 510 and 378 proteins were identified to be significantly changed in the OE lines under control, salt, and drought conditions, respectively. Most increased proteins were involved in various processes including Calvin cycle, citric acid cycle, glycolysis, and antioxidant pathways. Some were found to participate in ABA biosynthesis or response. Metabolomics revealed that many metabolites and phytohormones in OE were involved in plant growth and development. Also, ABA was increased in OE lines under control, salt, and drought conditions. Yeast one-hybrid analysis showed that McHB7 can bind to ERD and ABA-related motifs. And protein-protein interaction analysis discovered the candidate proteins that were responsive to stresses and hormones (e.g., ABA).
2024-05-21 | PXD033521 | Pride
Project description:We used the rhesus macaque model to study the effects of the cag pathogenicity island (cag PAI) on the H. pylori host-pathogen interaction. Specific pathogen free (SPF) monkeys with no prior exposure to H. pylori were experimentally challenged with wild type (WT) H. pylori strain J166 (N=4) or its cag PAI isogenic knockout (KO, N=4). Animals underwent endoscopy before and 1, 4, 8, and 13 wks after challenge. Gastric biopsies were collected for quantitative culture, histopathology, and host gene expression. Quantitative cultures showed that all experimentally challenged animals were infected with WT H. pylori or its isogenic cag PAI KO. Histopathology demonstrated that inflammation and expansion of the lamina propria were attenuated in animals infected with KO compared to WT. Microarray analysis was performed on challenged animals before and 1 and 13 wks after challenge, and on unchallenged control animals (N=4). Of the 119 up-regulated genes in the WT-infected animals, several encode innate antimicrobial effector proteins, including elafin, siderocalin, DMBT, DUOX2, and several novel paralogues of human defensin-2. Quantitative RT-PCR analysis showed that high level induction of each of these genes was dependent upon the presence of the cag PAI. Immunohistochemistry confirmed increased defensin epithelial cell staining in animals challenged with WT H. pylori compared to either KO-challenged or uninfected control animals. We propose that one function of the cag PAI is to induce an antimicrobial host response that serves to increase the competitive advantage of H. pylori in the gastric niche. Keywords: Transcript profiling , Wild type H. pylori, cag-PAI KO H. pylori
2008-02-01 | GSE8749 | GEO
Project description:Huntington’s disease (HD) is caused by CAG repeat expansion at the N-terminal region of huntingtin (HTT) gene and characterize by neuronal cell loss and neuroinflammation transcriptional profile change in striatum, cortex and other brain regions. Here we reported generation and characterization of BAC-CAG, a novel full length human HD mouse model host over 120 uninterrupted CAG repeats. we performed RNA-seq analysis of the striatum and cortex of BAC-CAG mice at 2m, 6m and 12m of age (N=6 per genotype, sex balanced). We observed an age-dependent transcriptionopathy in the striatum of BAC-CAG mice, with only 7 and 36 significant DE genes in 2m and 6m striatum respectively (FDR<0.1), but 820 DE genes (538 downregulated and 282 upregulated genes) at 12m of age (FDR<0.1). The transcriptomic deficits in this model are highly striatum-selective, as we only detected 4, 3 and 14 DE genes (FDR<0.1) at 2m, 6m and 12m respectively in BAC-CAG cortices compared to WT controls. Remarkably, we found a highly significant positive transcriptome-wide correlation (r=0.62) of DE Z statistics between BAC-CAG vs WT at 12m and Q140 vs WT at 6m (p<1e-200). This result demonstrates a high concordance of both upregulated and downregulated genes in the BAC-CAG striatum compared to that of allelic series KI mice; but RNA-seq studies of BACHD mice at 12m and found only 50 genes significantly differentially expressed (DE) genes (FDR<0.1) in the striatum at 12m of age compared to WT littermates, 31 downregulated and 19 upregulated genes. In the cortex at 12m of age, BACHD only showed 6 significantly downregulated genes and 7 upregulated genes comapred to WT controls (FDR<0.1).
2022-02-02 | GSE153827 | GEO
Project description:Purpose: To further identify the genes and pathways involved in the necrotic phenotype of NtCBL5A-OE lines, the leaf transcriptome profiling of WT and OE-2 lines grown under control conditions and salt stress (100 mM NaCl) at 4 DAT were sequenced and compared. Methods: Two datasets of differentially expressed genes (DEGs) were made in which we identified the genes that were differentially expressed as a result of the overexpression of NtCBL5A: Control-WT vs Control-OE2 (C-WT/C-OE2), Salt-WT vs Salt-OE2 (S-WT/S-OE2). Another two datasets were also used to identify the transcripts that were responsive to the salt treatments: Control-WT vs Salt-WT (C-WT/S-WT) and Control-OE2 vs Salt-OE2 (C-OE2/S-OE2). DEGs from C-WT/C-OE2 and S-WT/S-OE2 were compared to select the transcripts affected by NtCBL5A overexpression only under salt stress. We also compared DEGs from C-WT/S-WT and C-OE2/S-OE2 to identify the specific transcripts affected by salt stress and only in NtCBL5A-OE lines. This procedure was done for two independent experiments, and only DEGs that were identified in both experiments were considered. Results: The OE-affected DEGs and salt-affected DEGs together resulted in 2079 up-regulated DEGs and 1154 down-regulated DEGs, strongly affected by the combination of NtCBL5A overexpression and salt stress.
2021-08-17 | GSE181164 | GEO
Project description:This study was designed to identify changes in gene expression that occur when corn was grown on different landscape features. Specifically on the backslope or summit/shoulder of a hill. In rolling landscapes, plant available water varies drastically by location and soil type. Almost simultaneously, plants may be flooded out in footslope locations whereas plants in summit locations may be suffering from severe drought. The objective of this study was to determine the influence of landscape position on corn (Zea mays) productivity and gene regulation. Corn was sampled at V12 for plant growth characteristics and transcriptome analysis at summit/shoulder and lower backslope positions. Plants at the summit had 16% less leaf area and biomass compared with plants at the toeslope. Gene expression analysis using microarray chips, transcriptome analysis, and qPCR indicated that plants at the summit had 708 genes down-regulated and 399 genes up-regulated compared to control plants at the lower back slope. GSEA (Gene Set Enrichment Analysis) indicated tolerance to cold, salt, and drying were increased in summit/should plants compared to control toeslope plants. However, nutrient uptake, recovery from wounding, pest and fungal disease resistance, along with photosynthetic capacity were all down-regulated in moderate water stresses plants. These responses suggest that corn preferentially responses to water stress as the expense of its ability to respond to other stresses. Three biological replicates for the control (backslope) and six biological replicate of summit/shoulder-grown plants were collected. The resulting labeled cDNA was hybridized to the 46,000-element maize microarray chip developed by the University of Arizona using their protocol (International Microarray Workshop Handbook, 2009Gardiner et al. 2005). The hybridization scheme was a dual hybridization using a rolling circle balanced dye swap design. Thus we had three to six biological replicates for each growth condition and two technical replicates for each biological sample.
2011-11-05 | E-GEOD-33494 | biostudies-arrayexpress
Project description:We found different genes change between WT and OE cells.
2023-06-15 | GSE181017 | GEO
Project description:Discovery proteomics on three R. toruloides strains with differing Pnt1 expression (WT IFO 0880, OE-Pnt1, and delta Pnt1) grown on either xylose or xylose and glycerol at mid-log phase.
2022-07-21 | MSV000089938 | MassIVE