Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq of intestinal epithelial cells transfected with an siRNA targeting the host long noncoding RNA, NR_033483, or a scrambled siRNA control, with or without Cryptosporidium infection

ABSTRACT: Cryptosporidium is a protozoan parasite that infects the gastrointestinal tract of humans and animals. It is an important opportunistic pathogen in children under the age of two and immunocompromised adults. There is currently no fully effective therapy or vaccine. Long noncoding RNAs are RNA transcripts, over 200 nt in length, that are capable of regulating gene expression through both transcriptional and translational methods. Our lab previously identified a panel of host long noncoding RNAs are that upregulated during Cryptosporidium infection, including NR_033483. Further experiments indicated this host long noncoding RNA may be playing a pro-parasitic role during infection. We hypothesized that NR_033483 is regulating the expression of host immune genes to aid the parasite. In this study, we treated intestinal epithelial cells with an siRNA targeting NR_033483 to knockdown its expression, or a scrambled siRNA control, and infected the samples with Cryptosporidium. We sought to determine changes in host gene expression when NR_033483 was knocked down verse control samples.

INSTRUMENT(S): BGISEQ-500

ORGANISM(S): Mus musculus

SUBMITTER: Marion Graham

PROVIDER: E-MTAB-12972 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Vanee2010 - Genome-scale metabolic model of Cryptosporidium hominis (iNV213) This model is described in the article: A genome-scale metabolic model of Cryptosporidium hominis. Vanee N, Roberts SB, Fong SS, Manque P, Buck GA. Chem. Biodivers. 2010 May; 7(5): 1026-1039 Abstract: The apicomplexan Cryptosporidium is a protozoan parasite of humans and other mammals. Cryptosporidium species cause acute gastroenteritis and diarrheal disease in healthy humans and animals, and cause life-threatening infection in immunocompromised individuals such as people with AIDS. The parasite has a one-host life cycle and commonly invades intestinal epithelial cells. The current genome annotation of C. hominis, the most serious human pathogen, predicts 3884 genes of which ca. 1581 have predicted functional annotations. Using a combination of bioinformatics analysis, biochemical evidence, and high-throughput data, we have constructed a genome-scale metabolic model of C. hominis. The model is comprised of 213 gene-associated enzymes involved in 540 reactions among the major metabolic pathways and provides a link between the genotype and the phenotype of the organism, making it possible to study and predict behavior based upon genome content. This model was also used to analyze the two life stages of the parasite by integrating the stage-specific proteomic data for oocyst and sporozoite stages. Overall, this model provides a computational framework to systematically study and analyze various functional behaviors of C. hominis with respect to its life cycle and pathogenicity. This model is hosted on BioModels Database and identified by: MODEL1507180071. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

RNA-seq of intestinal epithelial cells transfected with an siRNA targeting the host long noncoding RNA, NR_033483, or a scrambled siRNA control, with or without Cryptosporidium infection

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