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Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

ABSTRACT: This RNA-seq study in primary human forekin keratinocytes was to define genes that are differetially expressed in the presence or absence of HPV18 E7 or the HPV18 E7 R84S variant.

ORGANISM(S): Homo sapiens

PROVIDER: GSE150201 | GEO | 2020/06/09

REPOSITORIES: GEO

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Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV16 E7

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Analysis of gene expression in primary human foreskin keratinocytes (HFK) +/- HPV18 E7

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The impact of HPV16 and HPV18 E6/E7 oncogenes on gene expression in non-tumorigenic keratinocytes (HaCaT cells)

Project description:This analysis aimed to identify differentially expressed genes in non-tumorigenic keratinocytes transduced with E6/E7 oncogenes of HPV16 or 18. The working cell models were named HaCaT E6/E7 HPV16, HaCaT E6/E7 HPV18, and HaCaT pLVX (empty lentiviral vector) as controls. mRNA sequencing was performed on the Illumina NovaSeq 6000 platform by Novogene Bioinformatics Technology Co., Ltd, Beijing, China, with two independent replicate sequences for each cell model. Methodology: The bioinformatics pipeline analysis was executed as described below: Rstudio (v2023.06.1+524) and Galaxy (https://www.usegalaxy.orgaccessed on 15 August 2023) open-source platforms were used to analyze the Illumina raw data. The Quality Check was performed through the FastQC tool (v0.12.1); afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p14 v43). The resulting output was the BAM files, of which the number of reads was counted by the featureCounts tool (v2.0.3); at the final step, the Differential Expression Analysis was settled by DESeq2 tool (v2.11.40.8). The differential gene expression measurements were normalized by DESeq2´s median of ratios (median of ratio of gene counts relative to geometric mean per gene) method. All chemokine genes with an adjusted p-value (adj p) ≤ 0.05 and fold change (Log2FC) > 1 .5 or < -1.5 were selected as differentially expressed genes (DEGs). Some genes from the resulting outputs were validated through qPCR. Conclusions: Our study found 3296 differentially expressed genes in HaCaT E6/E7 HPV16 and 1943 in HaCaT E6/E7 HPV18. These results suggest that E6/E7 oncogenes from HPV16 and 18 can broadly modify transcriptomic expression.

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Transcription profiling of human foreskin keratinocytes expressing E6 or E7 compared to normal keratinocytes reveals HPV16 E7 induces EMT

Project description:Gene expression data from human foreskin keratinocytes expressing E6 or E7 compared to normal keratinocytes.

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Effect of HPV8-E7 expression on the phospho-proteome in keratinocytes

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MicroRNA expression profile in human foreskin keratinocytes (HFKs) transduced with retroviral vectors carrying E6 and E7 genes of either HPV6 or HPV16 and with the LXSN empty vector

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