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Cetacean metagenome

ABSTRACT: 16S rDNA amplicon sequencing of the oral cavity microbiome of the common dolphin, harbour porpoise and stripped dolphin

PROVIDER: PRJNA494623 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7963810_1.fastq.gz	Fastqsanger.gz
	SRR7963810_2.fastq.gz	Fastqsanger.gz
	SRR7963820_1.fastq.gz	Fastqsanger.gz
	SRR7963820_2.fastq.gz	Fastqsanger.gz
	SRR7963830_1.fastq.gz	Fastqsanger.gz

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Project description:The Kaposi sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi sarcoma (KS), the most common HIV/AIDS-associated tumor worldwide. Involvement of the oral cavity portends a poor prognosis for patients with KS, but mechanisms for KSHV regulation of the oral tumor microenvironment are largely unknown. Infiltrating fibroblasts are found with KS lesions, and KSHV establishes latent infection within human primary fibroblasts in vitro, but contributions for KSHV-infected fibroblasts to the KS microenvironment have not been previously characterized. In the present study, we used Illumina microarray to detect the global gene profile altered in KSHV-infected primary human fibroblasts (PDLF and HGF) isolated from the oral cavity.

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Oral shedding of an oncogenic virus alters signatures of oral microbiome in HIV+ patients

Project description:Collectively, viruses are the principal cause of cancers arising in patients with immune dysfunction, including HIV+ patients. Kaposi’s Sarcoma (KS) etiologically linked to KSHV continues to be the most common AIDS-associated tumor. The involvement of oral cavity represents one of the most common clinical manifestations of this tumor. HIV infection incurs an increased risk for periodontal diseases and oral carriage from a variety of pathogenic bacteria. In the current study, by using 16S rRNA based pyrosequencing, we found that oral shedding of KSHV altered oral microbiota signature in HIV+ patients which may contribute to virus-associated malignancies development.

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Changes in RNA expression in human oral cavity carcinoma cells as a result of LDB1 reduction

Project description:The study was designed to identify differential expressed genes between human oral cavity carcinoma cell lines with and without LDBI knockout Three parental human oral cavity carcinoma cell lines were used as control, LDB1 was knocked out in the three parent cell lines to create KO cell lines.

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Project description:Genome wide high resolution assay of copy number in a series of frozen, microdissected head and neck cancers originating from the oral cavity. The objective was to characterize areas of amplification and deletion in head and neck cancers arising from the oral cavity subsite.

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Oral Cavity Cancer Compared to Adjacent "Normal" Tissue [Validation Set]

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Whole exome sequencing and transcription profiling of a patient cohort of oral cavity squamous cell carcinomas

Project description:Oral cavity Squamous Cell Carcinoma (OCSCC) is a common form of head and neck cancer through the developed and developing world. However, the etiology of OCSCC is still unclear. To explore whether smoking, HPV and/or other underlying genetic and transcriptomic changes could be responsible for the oncogenesis events for OCSCC. A prospective observational study of fresh tissue biopsy from 45 participants with OCSCC collected from Brisbane Head and Neck Clinics between 2013 to 2015. Exploration of the genetic and transcriptomic landscape was performed using RNA sequencing and whole exome sequencing. Identification of HPV was to be performed using DNA PCR genotyping and RNA sequencing. Patient medical records were retrieved and the patient demographics were used to correlate with genomic and transcriptomics analyses, including the location of the tumor within the oral cavity, smoking and alcohol histories.

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Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent. The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F

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Normal Oral Transcriptome

Project description:Three SAGE libraries brushed from the surface of the tongue and three SAGE libraries extracted from oral biopsies define the normal oral transcriptome. Keywords: SAGE, normal oral Six SAGE libraries isolated from the oral cavity were used to define the oral transcriptome.

2008-11-21 | E-GEOD-8127 | biostudies-arrayexpress

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