Transcriptomics of human adenocarcinoma cell line HCT-8 infected with Cryptosporidium parvum treated with indole
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ABSTRACT:
PROVIDER: PRJNA770275 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16290076_1.fastq.gz | Fastqsanger.gz | |||
| SRR16290076_2.fastq.gz | Fastqsanger.gz | |||
| SRR16290077_1.fastq.gz | Fastqsanger.gz | |||
| SRR16290077_2.fastq.gz | Fastqsanger.gz | |||
| SRR16290078_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goal of this study was to identify transcriptional changes in HCT-8 cells treated with indole for 4 or 12 hours. Methods: Confluent HCT-8 monolayers were infected with excysted Cryptosporidium parvum sporozoites for 4 h, after which cells were washed to remove extracellular parasites. Cells were then treated with 1% DMSO in cell culture medium with or without 880 uM indole. RNA was collected in triplicate for each treatment type after 4 h and 12 h of treatment (8 and 16 hours post infection, respectively). Results: When the two time points were combined, indole significantly upregulated 57 genes and downregulated 11 genes. Of the upregulated genes,16 genes were primarily upregulated in cells exposed to indole for 4 h and then went back down by 12 h of exposure. These genes were primarily involved in pathways related to ER stress and the unfolded protein response (UPR). Conversely, 41 genes had higher gene expression after 12 h of indole exposure and were predominantly involved in membrane transport of carboxylic acids and amino acids. Conclusions: Indole treatment causes ER stress and upregulation of membrane transporters in a human adenocarcinoma cell line infected with Cryptosporidium parvum.
2021-10-13 | GSE185652 | GEO
Project description:Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. circular RNA (circRNA) was discovered to play key roles in many diseases, and the well-known regulatory mechanism for circRNAs is that act as miRNA sponges competitively binding to miRNAs to block miRNA-mRNA interaction. Here, using microarray assay, we investigated the expression profiles of circRNAs in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 178 circRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype.
2022-12-15 | GSE162990 | GEO
Project description:Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key regulators of parasitic diseases. Therefore, we used microarray, qPCR, and bioinformatic analyses to investigate the intestinal epithelial miRNA expression profile after Cryptosporidium parvum infection.Twenty miRNAs were differentially expressed after infection (four upregulated and 16 downregulated). Further analysis of the differentially expressed miRNAs revealed that many important cellular responses were triggered by Cryptosporidium parvum infection, including cell apoptosis and the inflammatory and immune responses.This study demonstrates for the first time that the miRNA expression profile of human intestinal epithelium cells is altered by C. parvum infection. This dysregulation of miRNA expression may contribute to the regulation of host biological processes in response to C. parvum infection, including cell apoptosis and the immune responses. These results provide new insight into the regulatory mechanisms of host miRNAs during cryptosporidiosis, which may offer potential targets for future C. parvum control strategies.
2018-12-23 | GSE95365 | GEO
Project description:Cryptosporidium parvum is one of the most important opportunistic enteric parasites, causing severe diarrhea in immunocomprised human and animals. However, few effective control agents were available for this parasite. Long non-coding RNA (lncRNA) was discovered to play key roles in many diseases through regulating the gene expression. Here, using microarray assay, we investigated the expression profiles of mRNA and lncRNA in HCT-8 cells after the infection of C. parvum IId subtype, the prevalent subtype of China. A total of 821 lncRNAs and 1,349 mRNAs were dysregulated expressed in HCT-8 cells at 24 h post infection (pi) of C. parvum IId subtype. Of them, all five types of lncRNAs were identified, including 302 of sense, 280 of antisense, 312 of intergenic, 44 of divergent, and 33 of intronic lncRNAs. Ten lncRNAs and ten mRNAs randomly selected were successfully confirmed the microarray results. The co-expression and target prediction analysis indicated 27 of mRNAs cis-regulated by 29 lncRNAs and 109 of coding genes trans-regulated by 114 lncRNAs. These predicted targets were enriched in pathways involved in the interaction between host and C. parvum, eg. hedgehog signaling pathway, Wnt signaling pathway and tight junction, suggesting that these aberrantly lncRNAs would play important regulating roles during infection of C. parvum IId subtype.
2018-07-19 | GSE111565 | GEO
Project description:• The origin of biological samples (In vitro infection of HCT-8 cells with Cryptosporidium parvum) Monolayers of the HCT-8 cells (ATCC CCL-244, American Type Culture Collection) were cultured in RPMI 1640 medium containing 10% fetal bovine serum and additional nutritional supplements. Cells in log phase were plated at 2×106 cells per 150 mm tissue culture dish and infected with sterilised Cryptosporidium parvum oocysts (Iowa strain). Purified oocysts were suspended in phosphate buffered saline, sterilised in 33% bleach for 7 min on ice, washed in Hank's buffered saline solution, and added to HCT-8 cultures at a ratio of one oocyst per cell. Following a 2 h excystation period at 37 °C, cells were washed with warm Hank's buffered saline solution, and cells were incubated in fresh supplemented media. Mock-infected cultures were treated identically, with the exception that oocysts were not added to the cultures. Three independent mock- and C. parvum-infected cultures were prepared for analysis. • The origin of mRNA samples At 6, 12, 24, 48, and 72h post-inoculation, cell culture media were removed and cultures were immediately lysed by the addition of 3.5 ml of Trizol® reagent (GIBCO BRL Life Technologies) directly to the culture plate. Total RNA was prepared as described by the manufacturer, and poly(A) mRNA was isolated using oligo-dT cellulose columns (Amersham Pharmacia Biotech). The qualities of total RNA and poly(A) mRNA preparations were assessed by Northern blot. • Protocols for conducting microarray hybridization Poly(A) mRNA was converted into ‘target’ suitable for hybridisation to Affymetrix microarray chips according to protocols provided by Affymetrix Inc. (Santa Clara, CA). Briefly, 2.0 g of poly(A) mRNA was reverse-transcribed to prepare double-stranded cDNA using T7-(dT)24 primer (GENSET Corp., La Jolla, CA) and Superscript II reverse transcriptase (GIBCO). Approximately 1 g of cDNA was used for in vitro transcription in the presence of biotinylated UTP and CTP using the Enzo BioArray High Yield RNA Transcript Labelling Kit (Enzo Diagnostics, Inc). This labelled cRNA was fragmented in 40 mM Tris–acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate at 94 °C for 35 min. The integrity of cRNA and the efficiency of fragmentation were monitored by Northern blot analysis (not shown). Fragmented biotinylated cRNA targets were hybridised to HG-U95Av2 chips (Affymetrix) that contain probe sets for 12,600 human gene/transcripts. Fifteen micrograms of fragmented cRNA and appropriate controls were hybridised to the chips at 45 °C for 16 h with constant rotation at 60 rev./min. The chips were subsequently washed and stained with streptavidin–phycoerythrin conjugate using the GeneChip Fluidics station protocol EukGE_WS2 (Affymetrix). Following washing and staining, microarray chips were scanned twice at 3 m resolution using a Hewlett-Packard confocal scanner and hybridisation intensities for each of the genes/transcripts were collected from scanned images. • Analysis of microarray data Gene expression data were initially analysed with the GeneChip® expression analysis software (Affymetrix Microarray Suite, version 5.0). The fluorescence intensity of the genes/transcripts was measured for each probe array and, to minimise discrepancies due to non-biological variations, normalised by global scaling to 1000. Further data analyses were performed using GeneSpring software (version 6.0; Silicon Genetics, Redwood City, CA). Per gene normalisation was applied in which the expression signal of each gene in C. parvum-infected cells (raw data) was normalised to the median of its measurements in the mock-infected samples (control); and the ratio of expression levels between mock and infected samples was calculated as the mean value of normalised signal vs. control signal among three replicates. To identify genes with significantly altered expression, a series of statistical analyses (filtering) were performed: cut-off values for ratio of expression levels 1.80 and 0.55 were used to filter genes with expression level fold changes greater than ±1.8 in all three independent samples. Genes with fold change variations >1.5 across the three samples were excluded. Furthermore, a ‘statistical group comparison’ using Student's t-test/ANOVA was conducted to compare mean expression levels between mock-infected and infected samples, and the genes with significant differential expression (P<0.05) were selected. Identified differentially expressed genes were then annotated using GeneSpring's ‘Build Simplified Ontology’ constructor which hierarchically groups genes into meaningful biological categories (gene lists) based on the Gene Ontology Consortium Classifications. Various lists of regulated genes were created by cross-referencing annotated gene lists and applying assorted statistical and visualisation methods. Keywords: time-course
2005-02-15 | GSE2077 | GEO
Project description:To better understand the detailed interaction between the host and Cryptosporidium parvum, a large scale label-free proteomics study was conducted to characterize the changes to the proteome induced by C. parvum infection.
2021-07-29 | PXD027634 |
Project description:Cryptosporidium parvum has been reported to induce digestive adenocarcinoma in a rodent model of chronic cryptosporidiosis. In the current study, the transcriptomes of C. parvum infected ileo-caecal regions of mice developing tumours were analysed to identifie potential genes involved in development of cancer
2021-12-29 | GSE188591 | GEO
Project description:Cryptosporidium parvum genetic crosses
| PRJNA1263880 | ENA