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Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

ABSTRACT: Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

PROVIDER: PRJNA563012 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10044503_1.fastq.gz	Fastqsanger.gz
	SRR10044503_2.fastq.gz	Fastqsanger.gz
	SRR10044504_1.fastq.gz	Fastqsanger.gz
	SRR10044504_2.fastq.gz	Fastqsanger.gz
	SRR10044505_1.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

Project description:Purpose: The goals of this study are to understand the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection and determine the differential expressed genes Methods: Transcriptional profiles of human tonsillar epithelial cells UT-SCC-60B and human tonsillar epithelial cells infected with EV71 were generated by next generation sequencing, in triplicate, using Illumina X-ten/NovaSeq. The sequence reads that passed quality filters were analyzed abundance of mRNA using StringTie, the FPKM values of genes and transcripts were calculated by Ballgown of R software, alternative splicing events were determined by rMATS Results: Using an optimized data analysis workflow, we mapped more than 36 million sequence reads per sample. Total 11137 gene counts and 26860 transcript counts were identified in human tonsillar epithelial cells, 11347 gene counts and 27994 transcript counts were identified in EV71-infected human tonsillar epithelial cells. Total 96 genes and 499 transcripts were down-regulated, 105 genes and 550 transcripts were up-regulated according the criteria that fold changes are more than 1.5, p value less is than 0.05 and mean of FPKM value is more than 0.5 to defined as the differential expressed genes or differential expressed transcripts. Total 11563 novel genes and 14927 novel transcripts were identified and 3266 novel transcripts had the potential coding probabilities. Finally, total 5742 genes occurred alternative splicing events. Conclusions: Our study represents the first detailed analysis of the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection, this results will provide novel insight into the interaction between human tonsillar epithelial cells and EV71

2019-08-31 | GSE136668 | GEO

delta-Np63 loss of function study in the HNSCC cell line UT-SCC-74A

Project description:delta-Np63 is highly expressed in squamous cell carcinoma of the head and neck (HNSCC). To evaluate its function in HNSCC we depleted delta-Np63 by siRNAs in the HNSCC cell line UT-SCC-74A. The transcriptome was analysed by cDNA microarray.

2016-01-14 | E-MTAB-3670 | biostudies-arrayexpress

Identification of the UT-A1 Urea Channel Interactome

Project description:The urea channel Slc14a2 (or UT-A1) mediates vasopressin-regulated urea transport across the inner medullary collecting duct (IMCD). Previously, UT-A1 was found to present in a high molecular weight complex, suggesting UT-A1 is involved in certain protein-protein interactions. The present study sought to identify the proteins that interact with UT-A1 in this complex for a better understanding of how UT-A1 is regulated. Rat IMCD suspensions were treated with or without V2 receptor agonist, dDAVP, followed by in-cell crosslinking using BSOCOES and detergent solubilization. Immunoprecipitation using Dynabeads coated with UT-A1 specific antibody successfully pulled down the UT-A1 proteins. In-gel digestion protocol was carried out to prepare samples for liquid chromatographic mass spectrometry analysis of tryptic peptides using a Velos-Orbitrap mass spectrometer. The peptides passing stringent spectral quality thresholds were quantified (label-free) to identify those with (UTA-1 antibody/preimmune IgG) >4. A total of 128 UT-A1 interacting proteins were identified. Gene Ontology analysis maps the distribution of these proteins throughout major cell compartments: endoplasmic reticulum, Golgi, endosomes, cytosol and plasma membrane. Among them are four protein kinases (Cdc42bpb, Phkb, Camk2d, Mtor) that play roles in vasopressin-regulated phosphorylation of UT-A1. Non-label quantification was also performed to determine the stoichiometry of UT-A3 with UT-A1, the result does not support an oligomeric complex formation of UT-A1/A3. In conclusion, we have provided a refined list of UT-A1 binding proteins which can be useful for further analysis of the vasopressin signaling pathway in regulation of UT-A1 in IMCD.

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EV71 proteomics - Analysis of EV71 infection progression using triple-SILAC-based proteomics approach

Project description:Enterovirus 71 (EV71), a member of Picornaviridae, causes severe neurological and systemic illness in children. To better understand the virus-host cell interactions, we performed a triple-SILAC-based quantitative proteomics study monitoring host cell proteome changes after EV71 infection. Based on the quantitative data for more than 4100 proteins, ~17% of the proteins were found as significantly changed (p<0.01) at either 8 or 20 hours post infection (h.p.i.). Five biological processes and seven protein classes showed significant differences. Functional screening of 9 regulated proteins discovered the regulatory role of CHCH2, a mitochondrial protein known as a transcriptional activator for cytochrome c oxidase (COX), in EV71 replication. Further studies showed that CHCH2 served as a negative regulator of innate immune responses.

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Expression profile of EV71-infection-responsive miRNAs

Project description:We attempted to identify potential miRNAs that can regulate viral replication by screening host miRNAs in EV71-infected RD cells. To compare the differential expression of miRNAs in EV71-infected cells at different time points, miRNA expression profiles were analyzed using Agilent Human MicroRNA Array chips. At 5 h p.i., the expression levels of most miRNAs in EV71-infected cells were not different from those of mock-infected cells. However, five miRNAs (miR-574-3p, miR-574-5p, miR-181d, miR-197, and miR-939) showed a miRNAs (miR-193a-3p and miR-324-5p) exhibited a increase in expression level in response to EV71 infection at 10 h p.i.

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Homo sapiens PBMCs: pre-vaccination (stimulation vs. no stimulation with EV71 antigen) vs. post-vaccination (stimulation vs. no stimulation with EV71 antigen)

Project description:To characterize the primary and recall responses to EV71 vaccines, PBMCs from 19 recipients before and after vaccination with EV71 vaccine were collected. 14 samples pre-vaccination and 16 samples post-vaccination were detected by microarray and their gene expression signatures after stimulation with EV71 antigen were compared.

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Project description:HT29 cells was infected with EV71 at MOI 1 or nil respectively and harvested at 36hpi We use miRNA microarray to profile and identify miRNA which are up or down regulated due to EV71 infection

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Project description:Chromosomal instability is a hallmark of cancer and genes that display abnormal expression in chromosomally aberrant regions are likely to be key players in tumor progression. Identifying such driver genes from high-throughput data requires computational methods that are capable of integrating data from several sources and thereby enhance the reliability of driver gene identification. Hence, several algorithms that integrate copy number and expression data have been developed but their relative performance has not been assessed so far. We have compared 10 algorithms that integrate high-throughput copy number and transcriptomics data using simulated, cancer cell line and primary tumor data. Our results show that there are significant differences between the methods and their performance decreases significantly with small sample sets. Head and neck squamous cell carcinoma (HNSCC) cell lines from the tongue (UT-SCC-21,UT-SCC-24B, UT-SCC-30, UT-SCC-67, UT-SCC-73, UT-SCC-76A, UT-SCC-81, UT-SCC-87,UT-SCC-95) and larynx (UT-SCC-8, UT-SCC-11, UT-SCC-75) were provided by the Department of Otorhinolaryngology-Head and Neck Surgery at the Turku University Central Hospital (Turku, Finland). HNSCC cell lines SCC-4, SCC-9, SCC-25 and human skin keratinocyte HPV-16 E6/E7 transformed cell line CCD1106 KERTr was ordered from American Type Culture Collection (ATCC; Manassas, VA) and cultured according to the ATCC recommendations.

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miRNA profiling of EV71 infected HT29 cells

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