Gene expression of UC organoids and UC model organoids (long-term inflammation model) derived from human colonic organoids
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE156806 | GEO | 2020/10/26
REPOSITORIES: GEO
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Project description:Gene expression of UC organoids and UC model organoids (long-term inflammation model) derived from human colonic organoids
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Project description:This dataset consists of RNA-sequencing of intestinal organoids at rest and after stimulation with the TLR5 ligand flagellin for 4 hours. The goal of this study was to understand the differential patterns of gene expression induced upon stimulation with a TLR ligand in small intestine organoids, colon organoids, and organoids that had been skewed to generate a higher proportion of Paneth cells.
2018-08-28 | GSE117772 | GEO
Project description:Purpose: Organoids are gaining more traction as physiologically relevant models for host physiology, but their transcriptional stability has not been identified over long term culture. Comparing this to its host-derived tissue and a transformed cell line of this intestinal location could provide insight into the stability and maintenance of cellular programs in vitro. Methods: Jejunum organoids were derived from 2 5-week old piglets, and grown separately in triplicate for 3 and 12 weeks. Tissue homogenate, organoids from both time points (divided in triplicate at start of experiment to monitor culture-dependent variability) and three IPEC-J2 passage rates were isolated for RNA using an RNEasy mini kit following manufacturers protocols. Results: RNA was enriched for PolyA and sequenced on an illumina sequencer. Reads were checked for quality, trimmed, and mapped following the tuxedo suite pipeline (modified to fit our parameters) and CLC Genomics Workbench to identify unknown gene locations. Conclusions: Organoids cultured for 12 weeks showed strong inter- and intra variability, congruence between independent cultures, and strong epithelial resemblance to host tissues. It further exemplified a more extensive transcriptome than IPEC-J2, showing more physiologically relevant genes
2020-03-13 | GSE146408 | GEO
Project description:The 16p11.2 is the most common copy number variant (CNV) associated with Autism Spectrum Disorder (ASD). We used patient-derived cerebral organoids to investigate neurodevelopmental pathways dysregulated by dosage changes of 16p11.2 CNV. To investigate molecular dysregulation in DEL and DUP organoids, we carried out RNA sequencing and Tandem Mass Tag mass spectrometry (TMT-MS) on 1-month and 3-month organoids from the same samples. In proteomic analyses, we quantified a total of 6126 proteins in 1-month and 5481 proteins in 3-month organoids, with 13 and 11 proteins from within 16p11.2 CNV, respectively. Transcriptomic and proteomic profiling of organoids identifies the key drivers of functional effect by 16p11.2 CNV during neocortical development.
2019-12-19 | MSV000084727 | MassIVE
Project description:The overall gene expression pattern of HPRT knockdown murine D3 stem cells during neuronal differentiation was invesitigated by microarray based gene expression analysis and the results were interpreted by GO, GSEA and signaling pathway analyses with GeneSpring GX and PANTHER Classification System. For microarray experiment, total RNAs from replicated HPRT knockdown and control cultures were pooled and the microarray experiment with each pooled sample was triplicated, respectively.
2012-11-22 | E-GEOD-42453 | biostudies-arrayexpress
Project description:To characterize mechanisms responsible for the CNS dopamine deficiency and the resulting neuropathology caused by deficiency of the housekeeping purine salvage function hypoxanthine guanine phospho- ribosyltransferase (HPRT) in the Lesch Nyhan Disease (LND), we have used microarray-based methods of global gene expression together with quantitative PCR and Western blot analysis to identify dysregulation of genes and aberrant cellular processes in human fibroblasts and in SH-SY5Y neuroblastoma cells made HPRT-deficient by transduction with a retrovirus stably expressing an shRNA targeted against HPRT. Analysis of the microarray expression data by Gene ontology (GO) and Gene Set Enrichment Analysis (GSEA) as well as by GeneSpring GX10 and Panther Classification System reveal that HPRT deficiency is accompanied by aberrations in a variety of pathways known to regulate neurogenesis or to be implicated in neurodegenerative disease, including the canonical Wnt/β-catenin and the Alzheimer’s disease/presenilin signaling pathways. Dysregulation of the Wnt/β-catenin pathway is confirmed by Western blot demonstration of cytosolic sequestration of β-catenin during in vitro differentiation of the SH-SY5Y cells toward the neuronal phenotype. We also demonstrate that two key transcription factor genes known to be regulated by Wnt signaling and to be vital for the generation and function of dopaminergic neurons; i.e., Lmx1a and Engrailed 1, are down-regulated in the HPRT knockdown SH-SY5Y cells. In addition to the Wnt signaling aberration, we found that expression of presenilin-1 shows a severely disturbed expression in HPRT-deficient cells, reflected by marked instability of the 23kDa C-terminal fragment of presenilin-1 in knockdown cells. Western blot analysis of primary cultures of two LND patients with 2.5% and 0% residual HPRT activity also shows dysregulated b-catenin and presenilin-1 expression, including elevated levels of cytosolic phospho-catenin and, in one of the two patient cells, failure of nuclear transport. Similarly, the presenilin-1 processing defect was most clearly demonstrated by markedly increased levels of both the N-terminal and C-terminal presenilin-1 fragments in the human cell line with no detectable residual enzyme activity but less marked over-expression in the cell with 2.5% residual enzyme activity. These demonstrations of dysregulated Wnt and presenilin-1 signaling and impaired expression of transcription factors necessary for dopaminergic development reveal broad pleitropic neuro-regulatory defects played by HPRT and suggest new directions for investigating mechanisms of aberrant neurogenesis and neuropathology in LND and potential new targets for restoration of effective signaling in this neuro-developmental defect. For microarray analysis, RNAs from triplicate independent cultures of vector-infected HPRT knockdown and control fibroblasts were prepared separately, pooled and used to prepare cRNA and finally subjected to microarray transcriptional analysis in triplicate. The integrity of total RNA from HPRT knockdown and control cells was confirmed by bioanalyzer (Agilent Technologies, Santa Clara, CA). The quality of total RNA samples from HPRT knockdown and control cells was assessed by 2100 bioanalyzer before application to microarray analysis. We determined that the RNA integrity number (RIN), (maximal degradation = 1; maximal molecular integrity = 10) was 10 for both the normal and knockdown cells (data not shown), indicating that isolated RNA samples were of sufficiently high quality to permit subsequent preparation of cDNA for microarray analysis. Microarray transcriptional analysis was performed in triplicate using the HumanWG-6 v3.0 Expression BeadChip system (Illumina, San Diego, CA). All reagents were obtained from HumanWG-6 v.3 Expression BeadChip Kit (Illumina) and all experimental processes were carried out according to manufacturer’s instruction (Illumina). After scanning of hybridized BeadChip, quantitation of slide images were performed using Illumina’s BeadArray software and the raw data were normalized by Loess normalization method, and then the normalized raw data in BeadStudio was exported to GeneSpring GX 10.0.2 (Agilent, Santa Clara, CA). For identification of genes significantly altered in knockdown cell compared with the control normal gene set, total detected entities were filtered by signal intensity value (upper cut-off 100th and lower cut-off 20th percentile) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, t-test unpaired (p < 0.05) was applied and all significant changes above 2-fold were selected. Signals were selected if they were above microarray background (detection p-value < 0.05) in either all six experiments or in at least three knockdown or control experiments. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 10.0.2 (Agilent) and the PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using GeneSpring GX 10.0.2 (Agilent), a total of 140 cellular pathways were identified. For GSEA analysis, we used the false discovery rate (FDR) of <0.4 and p ≤ 0.1.
2010-09-25 | E-GEOD-24345 | biostudies-arrayexpress
Project description:The overall gene expression pattern of HPRT knockdown murine D3 stem cells during neuronal differentiation was invesitigated by microarray based gene expression analysis and the results were interpreted by GO, GSEA and signaling pathway analyses with GeneSpring GX and PANTHER Classification System.
2012-11-22 | GSE42453 | GEO
Project description:We established murine fallopian tube epithelial organoids from a B6J.129(B6N)-Gt(ROSA)26Sortm1(CAG-cas9*,-EGFP)Fezh/J mouse. Subsequently, we knocked out Trp53 by introducing sgRNA into the organoids, nutlin-3 selection, and single-organoid cloning. The Trp53-knocked organoids grew faster than the normal organoids. We also analyzed the transcriptomic differences caused by Trp53-knockout by RNA-sequencing and gene set enrichment analysis (GSEA), which indicated that Trp53-knockout reduced cilium-related gene expression. In human HGSC precancerous lesions, such as serous tubal intraepithelial carcinoma (STIC), differentiation to ciliated cells has been reported to be down-regulated; therefore, the genetic manipulation was supposed to mimic the process of carcinogenesis of HGSC.
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Project description:Human liver organoids, an in vitro 3D culture system to recapitulate biological tissue, are expected to be used for drug discovery. However, Matrigel, the most widely used extracellular matrix for organoid culture, has concerns about safety and reproducibility since it is murine-derived. Morever, low hepatic functions of human liver organoids compared to primary human hepatocytes is considered a challenge. Herein, we attempted to culture human liver organoids, established from primary (cryopreserved) human hepatocytes (PHH), using HYDROX, a chemically defined 3D nanofiber. While proliferative capacity of human liver organoids was lost by HYDROX-culture, the gene expression level of a hepatocyte marker CYP3A4 and the CYP3A4 metabolic activity in HYDROX-cultured liver organoids were significantly improved, comparable to those of PHH. HYDROX-cultured liver organoids when treated with hepatotoxic drugs such as acetaminophen showed similar cell viability to that of PHH, suggesting that HYDROX-cultured liver organoids could be applied to drug-induced hepatotoxicity test. Furthermore, HYDROX-cultured liver organoids maintained its functions for up to 35 days and could be used to estimate chronic drug-induced hepatotoxicity such as those of fialuridine. Our findings demonstrated that human liver organoids obtained high liver functions by HYDROX-culture, meaning that HYDROX could contribute to drug discovery as a novel biomaterial.
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