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The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq knock-down]

ABSTRACT: The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq knock-down]

PROVIDER: PRJNA432253 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6654152.fastq.gz	Fastqsanger.gz
	SRR6654153.fastq.gz	Fastqsanger.gz
	SRR6654154.fastq.gz	Fastqsanger.gz
	SRR6654155.fastq.gz	Fastqsanger.gz
	SRR6654156.fastq.gz	Fastqsanger.gz

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The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma

Project description:The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma

| PRJNA432255 | ENA

The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq knock-down]

Project description:RNA-Sequencing Analysis of gene expression changes due to ablation of Ets1 in SCC25 Cells.

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The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [ChIP-seq]

Project description:The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [ChIP-seq]

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The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [ChIP-seq]

Project description:Mapping the genome-wide binding profile of ETS1 in a Mesenchymal HNSCC Cell Line using ChIP-Seq techniques

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The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq Cell lines]

Project description:The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq Cell lines]

| PRJNA432254 | ENA

Molecular Subtypes in Head and Neck Cancer [expression]

2013-03-01 | GSE39366 | GEO

Molecular Subtypes in Head and Neck Cancer [expression]

Project description:Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease whose underlying etiology has not been explained by traditional prognostic factors such as tumor site, stage, or histology. Although previous studies have shown that molecular subtypes of HNSCC exist, the benefit of such a classification scheme has not been fully realized. We show that molecular subtypes of HNSCC exist; that these subtypes have distinct patterns of chromosomal gain and loss, some of which affect canonical oncogenes and tumor suppressors; and that the subtypes are biologically and clinically relevant. These subtypes provide new insight into HNSCC etiology, as well as a valuable method for classifying HNSCC tumors. A total of 163 samples were considered. Quality control procedures were applied to microarray probe-level intensity files. A total of 138 tumor arrays remained after removing low-quality arrays, duplicate arrays, and arrays from non-HNSCC samples. The normexp background correction and loess normalization procedures were applied to the probe-level data. After log transformation, probes were matched to a common gene database to produce expression values for 15595 genes.

2013-03-01 | E-GEOD-39366 | biostudies-arrayexpress

Molecular Subtypes in Head and Neck Cancer [copy number]

2013-03-01 | GSE39367 | GEO

Molecular Subtypes in Head and Neck Cancer [copy number]

Project description:Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease whose underlying etiology has not been explained by traditional prognostic factors such as tumor site, stage, or histology. Although previous studies have shown that molecular subtypes of HNSCC exist, the benefit of such a classification scheme has not been fully realized. We show that molecular subtypes of HNSCC exist; that these subtypes have distinct patterns of chromosomal gain and loss, some of which affect canonical oncogenes and tumor suppressors; and that the subtypes are biologically and clinically relevant. These subtypes provide new insight into HNSCC etiology, as well as a valuable method for classifying HNSCC tumors. A total of 141 samples were considered. CEL files were subject to quality control (QC) procedures using the Affymetrix Genotyping Console, and arrays that produced contrast QC measurements above the default threshold of .4 were removed from subsequent analysis. The remaining 99 CEL files were processed with aroma, and log2 intensity ratios were produced using a pooled collection of normal samples as a reference. After segmenting the log2 ratios with DNAcopy, the resulting copy number profiles were subjected to manual review. Arrays that produced low quality copy number profiles were removed from subsequent analysis. Copy number values from chr1 - chr22 were considered.

2013-03-01 | E-GEOD-39367 | biostudies-arrayexpress

The Molecular Dissection of the Oncogenic Role of ETS1 in the Mesenchymal Subtypes of Head and Neck Squamous Cell Carcinoma [RNA-seq Cell lines]

Project description:RNA-Sequencing Analysis was performed on 7 Head and Neck Squamous Cell Carcinoma Cells Lines in order to examine their overall gene expression profiles.

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