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Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [mRNA]

ABSTRACT: Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [mRNA]

PROVIDER: PRJNA786460 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17138962_1.fastq.gz	Fastqsanger.gz
	SRR17138962_2.fastq.gz	Fastqsanger.gz
	SRR17138963_1.fastq.gz	Fastqsanger.gz
	SRR17138963_2.fastq.gz	Fastqsanger.gz
	SRR17138964_1.fastq.gz	Fastqsanger.gz

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Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA]

Project description:Purpose: The current study used high-throughput sequencing technology and related basic experimental verification assays to evaluate new pathogenic mechanisms of Human papilloma virus HPV+ Head and neck squamous cell carcinoma (HNSCC) as well as to determine the potential therapeutic targets. Materials and methods: In this study 3 pairs of tissues were collected from patient with HPV+ and HPV- HNSCC for high-throughput sequencing analysis. After mRNA sequencing and analysis, multiple bioinformatics methods, real-time quantitative reverse transcription-quantitative polymerase chain reaction (qRT-PCR) and immunehistochemical verification assays were carried out to evaluate the potential therapeutic targets of HNSCC (CKAP5). The CKAP5 was then used to further predict the circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA). Sequencing analysis was also performed to further evaluate the potential carcinogenic pathway. Human papilloma virus detection was carried out through Enzyme-Linked Immune Sorbent Assay (ELISA) and the RT-PCR. Results: Results of high-throughput sequencing analysis, related databases, and verification of qRT-PCR at the cell and tissue level, revealed that the expression level of CKAP5 in HPV+HNSCC was significantly higher than that in HPV-HNSCC. Further, a competitive endogenous RNA (ceRNA) network was also constructed through the analysis of Miranda, multiMiR, lncBase prediction, and sequencing technology. The constructed ceRNA consisted of 1 mRNA, 2 miRNAs, and 1 lncRNA, and 6 CircRNAs. This was verified by RNA22, whereby the relationship between miR-155-5p and CKAP5 was found to be important whereas the hsa_circ_00058495 was a key circRNA according to the binding site scores. Conclusion: In conclusion it was evident that Hsa_circ_00058495/miR-155-5p CKAP5 may be an important pathway which is involved in the occurrence and development of HPV+ HNSCC.

2021-12-08 | GSE190223 | GEO

Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [mRNA]

2021-12-08 | GSE190222 | GEO

Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation

Project description:Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation

| PRJNA786457 | ENA

Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA]

Project description:Competing endogenous RNA analysis reveals the regulatory potency of CKAP5 in HPV+ HNSCC based on high throughput sequencing technology and clinical validation [miRNA]

| PRJNA786459 | ENA

Methylome Analysis of FF HPV+ and HPV- HNSCC samples

Project description:The analysis of the 6 methylomes by MeDIP-Seq comprise 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples Analysis of the 6 methylomes, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-01 | E-GEOD-38263 | biostudies-arrayexpress

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 42 450k methylation profiles, comprising 21 HPV+ HNSCC samples and 21 HPV- HNSCC samples

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Methylome Analysis of FF HPV+ and HPV- HNSCC samples

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450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip Analysis of 6 450k methylation profiles, comprising 3 HPV+ HNSCC samples and 3 HPV- HNSCC samples

2012-11-30 | E-GEOD-38268 | biostudies-arrayexpress

450k Analysis of 42 FFPE HPV+ and HPV- HNSCC samples

Project description:The methylation analysis of 21 FFPE HPV+ HNSCC samples and 21 FPPE HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38266 | GEO

450k Analysis of 3 FF HPV+ and 3 FF HPV- HNSCC samples

Project description:The methylation analysis of 3 FF HPV+ HNSCC samples and 21 FP HPV- HNSCC samples by Infinium HumanMethylation450 BeadChip

2012-11-30 | GSE38268 | GEO