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The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs

ABSTRACT: The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs

PROVIDER: PRJNA686003 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13266947.fastq.gz	Fastqsanger.gz
	SRR13266948.fastq.gz	Fastqsanger.gz
	SRR13266949.fastq.gz	Fastqsanger.gz
	SRR13266950.fastq.gz	Fastqsanger.gz
	SRR13266951.fastq.gz	Fastqsanger.gz

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Project description:Objective: Seek the differentially expressed mRNAs and long non-coding RNAs (LncRNAs) to construct the modulated network and seek for the hub LncRNAs during the process of human immunodeficiency virus (HIV) transcription. Method: Blood samples from HIV-infections were collected. They were divided into transcription active group and relatively inactive group based on the quantitative detection results of total HIV DNA and cell-association RNA (CA-RNA) from peripheral blood mononuclear cells (PBMCs). Individuals within each group were matched by age and genders. Microarray chips detection technology were utilized to detect and find the differentially expressed LncRNAs and mRNAs by statistical method of paired T test, then underwent some bioinformatics analysis. Result: 1240 differentially expressed genes (include 689 LncRNAs and 551 mRNAs) were found. Gene ontology analysis showed the differentially expressed mRNAs mainly enriched in positive or negative gene expression, immune cell formation or epigenetic regulation in the biological process; nucleosome, nucleolus, cytoplasm, nuclear chromatin in the cell component; RNA polymerase II regulatory region sequence-specific DNA binding, DNA, histone, and nucleic acid binding, transcription factor activity in molecular function. Pathway analysis showed the differentially expressed mRNAs enriched in the biological pathways such as systemic lupus erythematosus, alcoholism, cytokine-cytokine receptor interaction, RNA transport, mRNA surveillance pathway, Pathways in cancer, etc. Cis and trans analysis to the differentially expressed LncRNAs searching its targeted genes and then made intersection for the differentially expressed mRNAs, then constructed the modulated network between LncRNAs and mRNAs. Based on this modulated network, four hub transcripts were excavated and validated by quantitative real-time PCR to confirm the veracity of microarray analysis findings. Two hub transcripts of lnc-CCNYL1-1:2 and ZNF793 were found directly interacted in the modulated network and their level of expression transformed parallelly. Conclusion: Quantitative detection results of cellular levels of total HIV DNA and RNA can distinguish whether HIV is in the state of active transcription. During process of HIV transcription, the differentially expressed LncRNAs involve the biological process of gene expression regulation, the hub genes excavated form the modulated network may become the potential candidate targets for HIV antiviral treatment.

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The p53 transcriptional response across tumor types reveals core and outcome-specific signatures modulated by cis-regulatory lncRNAs

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