Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative transcriptome data of ARPE-19 cells with and without HTRA1 overexpression

ABSTRACT: To explore the key signaling pathways that might be affected by up-regulated HTRA1, we performed RNA-seq analysis on ARPE-19 cells infected with HTRA1 adenovirus and negative control adenovirus for 24 h. Compare with control groups, there were 2810 differentially expressed genes (log2 |fold change|> 1, log10 adjusted p-values < 0.05) were identified to be associated with distinct biological processes. 1053 genes were significantly upregulated and 1757 genes were significantly downregulated in ARPE-19 cells overexpressing HTRA1. The KEGG pathways analysis of up-regulated and down-regulated genes and ranking the enrichment pathways according to the corrected p-value. In the KEGG pathways analysis of up-regulated genes, the metabolic pathways ranked first with 84 genes involved. And in the KEGG pathways analysis of down-regulated genes, the metabolic pathways ranked third with 104 genes involved. These results revealed that up-regulated HTRA1 prominently disturbed the metabolic pathways in ARPE-19 cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE186816 | GEO | 2023/06/22

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Human RPE LC-MSMS

Project description:AMD is a complex disorder related to environmental factors and genetic polymorphisms. We explored the interplay between the two factors by comparing the differences between HTRA1/ARMS2 high-risk and low-risk AMD alleles after exposure to smokers’ serum using iTRAQ-based proteomics. Primary human retinal pigment epithelial (hRPE) cells were obtained from donor eyes and screened for ARMS2/HTRA1 AMD risk genotypes, wild type allele as control. A gene ontology annotation analysis and KEGG metabolic pathway analysis were employed to obtain a global functional view of differentially expressed (DE) proteins. Significant DE proteins were screened and validated by real-time PCR, immunofluorescence and western blot. The relationship between HTRA1 and caveolin-1 protein was explored by HTRA1-overexpressing lentivirus-transduced ARPE-19 cells. A total of 400 DE proteins were detected for the high-risk allele after cigarette sera stimulation, which was much higher than the low-risk allele. The caveolin-1 protein was significantly up-regulated when HTRA1-overexpressing cells were exposed to smokers’ serum and the smoking effect was stronger than AMD high-risk allele. There were interplays between AMD high-risk allele and cigarette smoking. Smokers’ sera also accelerated the phagocytosis of hRPE cells. In addition, caveolin-1 may play an important role in the disease process, but its molecular mechanism requires further study.

2022-02-22 | PXD009309 | Pride

Appropriately Differentiated ARPE-19 Cells Regain a Native Phenotype and Similar Gene Expression Profile

Project description:The retinal pigment epithelial (RPE) cell line ARPE-19 provides a widely-used alternative to native RPE. However, retention of the native RPE phenotype becomes problematic after multiple passages. We wished to determine if suitable culture conditions and differentiation could restore RPE-appropriate gene expression to ARPE-19. ARPE-19 cells at passages p9 to p12, grown in DMEM containing high glucose and pyruvate with 1% fetal bovine serum, were differentiated for up to 4 months. Using RNA-Seq, we compared the transcriptome of ARPE-19 cells kept in long-term culture with those cultured for 4 days. The 4 month cells developed the classic native RPE phenotype with heavy pigmentation. RNA-Seq analysis provided a comprehensive view of the relative abundance and differential expression of genes in the 4 month cells. Of the 16,757 genes with detectable signals, nearly 2435 genes were upregulated, and 931 genes were down-regulated with a fold change differences of 2 or more. Genes characteristic of RPE, including RPE65, RDH5 and RDH10, were greatly increased in ARPE-19 cells maintained at confluence for 4 months. Comparison with microarray data sets from human primary cell lines revealed important overall similarities in expression of "signature" genes. The results of this study demonstrate that ARPE-19 cells can express genes specific to native human RPE cells when appropriately cultured, and thus, can provide a relevant system to study differentiated cellular functions of RPE in vitro.

2017-04-12 | GSE88848 | GEO

Comparative transcriptome data of ARPE-19 cells with and without HTRA1 overexpression

Project description:Comparative transcriptome data of ARPE-19 cells with and without HTRA1 overexpression

| PRJNA776175 | ENA

Identification of the molecular basis of anti-cancer effect of Huaier.

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

Effect of metformin on mRNA expression in lung cancer cells

Project description:The genes whose transcription was significantly altered by metformin were investigated in H1299 cells by RNA-seq. Significantly up- or down-regulated genes were identified by cutoff value of |FC| >= 1.5. Metformin significantly downregulated mRNA levels of 499 genes while upregulating 615. KEGG (Kyoto Encyclopedia of Genes and Genomes) gene enrichment analysis revealed that the highly ranked clusters were cell cycle, apoptosis, cellular senescence and p53 signaling pathways. Multiple cell cycle checkpoint genes such as CCNA, CCNB, CCNE, CDK1, E2F2, E2F6, and E2F8 were downregulated, while certain cell cycle inhibitors such as CDKN2B (p15), CDKN1A (p21), DDIT4, and GADD45 were upregulated.

2019-11-27 | GSE141052 | GEO

Gene expression signitures in ARPE-19 cells treated with or without TGF-β1

Project description:To identify the dysregulated lncRNA and mRNA expression in ARPE-19 cells underwent EMT, we established a TGF-β1 induced EMT model of ARPE-19 cells. ARPE-19 cells were treated with or without 10 ng/ml TGF-β1 for 48 h. Total RNA are extracted and subjected to microarray assay (Arraystar Human LncRNA Microarray V3.0)

2021-08-11 | GSE105053 | GEO

Transcriptome profiling (RNA-seq) analysis of control and NaIO3-treated RPE cells

Project description:Purpose: The goal of this experiment is to investigate the relative contributions of various types of cell death in NaIO3-treated RPE cells Methods: RPE cell mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. Results: According to the differential expressions of mRNA genes, among which 661 genes were upregulated and 637 genes were downregulated with significance after NaIO3 treatment . From the Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, it has been identified that ferroptosis ranked as the top pathway in comparison to other types of cell death (apoptosis, and necroptosis) upon NaIO3 treatment, which was additionally validated by the higher FPKM of main regulators in ferroptosis than that in apoptosis. Additionally, it was found that heme oxygenase-1 (HMOX1, also known as HO-1) as well as SLC7A11 (solute carrier family 7 member 11) mRNA were characterized as the most dramatically upregulated genes upon NaIO3 treatment against ARPE-19 cells Conclusions: Our study represented that ferroptosis serves as a predominant pathogenic factor involved in AMD pathological process.

2019-12-26 | GSE142591 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Enterococcus durans A8-1 cells fermentation at MRS medium and MRS medium supplied with 60mg/L Na2SeO3

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

ARPE-19_adriamycin_gene_expression

Project description:This study compared the gene expression change of ARPE-19 cells before and after adriamycin treatment ARPE-19 cells were treated with 1Î¼M adriamycin for 24 h compared with control

2016-03-01 | E-GEOD-78765 | biostudies-arrayexpress

Expression Data from DMSO or SRPIN803 treated ARPE-19 cells

Project description:We used microarrays to evaluate the effect of SRPIN803 on gene expression in ARPE-19 cells. ARPE-19 cells were treated with SRPIN803 (10 uM) or the negative control (0.1% DMSO) for 4 hours for Total RNA isolation and hybridization on Microarray.

2015-06-17 | E-GEOD-62947 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data