Case control study comparing the microbiome and virome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing

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UID: 10752

Publisher(s): New York University - School of Medicine.

Description: Description from BioProject: "This is a case control study to compare oral microbiome and virome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing."
The study where the dataset originated from shows a case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma (OC-SCC) to normal patients using metagenomic shotgun sequencing.

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Oral Cavity Squamous Cell Carcinoma

Access via BioProject
WGS Sequencing of 9 experiments
Accession #: PRJNA692713
Access Restrictions: Free to All
Access Instructions: The NCBI BioProject and SRA databases provide open access to these files. SRA experiment files can be downloaded directly from the site or viewed in the NCBI SRA Run Selector.
Associated Publications: Ganly I, Pei Z, Hao Y, et al. Case control study comparing the HPV genome in patients with oral cavity squamous cell carcinoma to normal patients using metagenomic shotgun sequencing. Scientific Reports. 2021; 11:3867.
Data Type: Genomic
Equipment Used: Illumina HiSeq X Ten
Set of 10 ultra-high-throughput sequencers
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): BAM
Data Tool(s): WGS
Dataset Size: 1 MB

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