GEO DataSets

(Submitter supplied) Purpose: We aim to identify transcriptomic changes associated with EGFR-mediated epithelial to mesenchymal transition in carcinoma cells of the upper aerodigestive tract Method: Kyse30 and FaDu (ATCC, Manassas, VA, USA) were passaged in DMEM or RPMI, 10% FCS, 1% penicillin/streptomycin, 5% CO2 atmosphere at 37°C. Treatment with EGF (PromoCell PromoKine, Heidelberg, Germany), EpEX-Fc (Pan et al. PMID: 30261040) were conducted under serum-free conditions for 6h and 72h. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

84 Samples

Download data: TXT

(Submitter supplied) A miRs expression profiling of a total of 746 miRs (664 human + 82 viral) in 72 Head and Neck Squamous Cell Carcinoma (HNSCC) primary tumors to classify patients at high risk to develop recurrences

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18410

44 Samples

Download data: TXT

(Submitter supplied) Head and neck squamous cell carcinomas (HNSCC) are known to overexpress a variety of receptor tyrosine kinases, such as the HGF receptor Met. Like other malignancies, there is a mutual interaction between the tumor cells and surrounding tissues and cells. We hypothesized that activation of HGF/Met signaling in HNSCC might influence glucose metabolism and therefore substantially changes the tumor microenvironment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: CSV

(Submitter supplied) Gene expression analysis of primary HNSCC cell lines and their corresponding gefitinib resistant cell lines

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: XLS

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

26 Samples

Download data

(Submitter supplied) RNA-Sequencing Analysis of gene expression changes due to ablation of Ets1 in SCC25 Cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

8 Samples

Download data: TXT

(Submitter supplied) RNA-Sequencing Analysis was performed on 7 Head and Neck Squamous Cell Carcinoma Cells Lines in order to examine their overall gene expression profiles.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data

(Submitter supplied) Mapping the genome-wide binding profile of ETS1 in a Mesenchymal HNSCC Cell Line using ChIP-Seq techniques

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

3 Samples

Download data: BED

(Submitter supplied) Clinical outcome for patients suffering from head and neck squamous cell carcinoma (HNSCC) remains poor. This is mostly due to highly invasive tumors that cause loco-regional relapses after initial therapeutic intervention. The molecular pathways governing the detrimental invasive growth modes in HNSCC remain however understudied. Here, we have established HNSCC patient derived organoid (PDO) models that recapitulate 3-dimensional invasion in vitro. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: MTX, TSV

(Submitter supplied) Afatinib may augment pembrolizumab therapy and improve the ORR in HNSCC patients. The paired tissue analysis showed that afatinib, an epidermal growth factor (EGFR) tyrosine kinase inhibitor, may enhance antigen presentation, natural killer cell–mediated cytotoxicity, and immune reactions. We also identified unaltered methyl-thioadenosine phosphorylase (MTAP) levels, EGFR amplification, and high programmed death-ligand 1 expression as possible predictive biomarkers for therapeutic outcomes.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL31055

31 Samples

Download data: RCC

(Submitter supplied) Metformin is one of the first-line drugs for clinical treatment of type II diabetes, and recent studies have found that metformin can inhibit the development of multiple malignant tumors. When metformin is combined with chemotherapeutic drugs to treat head and neck squamous cell carcinoma（HNSCC）, it can effectively enhance the efficacy of chemotherapy. The aim of this study was to define the signaling pathways regulated by metformin in HNSCC, and the underlying mechanisms by which metformin sensitizes HNSCC chemotherapy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) RNA-Seq results suggested that epithelial to mesenchymal transition (EMT) -related pathways were upregulated in the metastatic subclones. Furthermore, forced expression of ST6Gal-I in the parental Suit2 line was sufficient to upregulate EMT, indicating a functional role for ST6Gal-I in this process.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

30 Samples

Download data: BED, BW, TDF

(Submitter supplied) Here, we performed ChIP-seq and ATAC-seq and identified two novel super enhancers (SE1 and SE2) responsible for EGFR transcription present within the first intron of the EGFR gene in HNSCC and GBM. SE1 and SE2 span 37kb and 33kb respectively, contain H3K27Ac enhancer histone marks and open chromatin, functionally enhance transcription in reporter assays, interact with the EGFR promoter, and negatively impact EGFR transcript levels and anchorage-independent growth when perturbed by CRISPR/Cas9-deletion and dCas9-KRAB-silencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: BED, TDF

(Submitter supplied) Here, we performed ChIP-seq and ATAC-seq and identified two novel super enhancers (SE1 and SE2) responsible for EGFR transcription present within the first intron of the EGFR gene in HNSCC and GBM. SE1 and SE2 span 37kb and 33kb respectively, contain H3K27Ac enhancer histone marks and open chromatin, functionally enhance transcription in reporter assays, interact with the EGFR promoter, and negatively impact EGFR transcript levels and anchorage-independent growth when perturbed by CRISPR/Cas9-deletion and dCas9-KRAB-silencing. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: BED, BW

(Submitter supplied) Head and neck squamous cell carcinoma (HNSCC) undergoes stepwise progression from normal tissue to metastasized tumors. To comprehensively delineate the heterogeneity of tumor cells and their interactions during the progression of HNSCC, we employed single-cell RNA-seq (scRNA-seq) profiling for the tissues of normal, leukoplakia, HNSCC, and metastasized HNSCC. We identified novel clones of malignant cells expressing LGALS7B and fibroblasts expressing CXCL8, and the abundance of these cells in the tumor tissue was associated with poorer prognostic outcomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

37 Samples

Download data: TXT

(Submitter supplied) We demonstrate that progression along EMT occurs along a continuum and that interruption of key signaling events reveals regulatory “barriers” that mimic discrete stages.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: MTX, RDS, TSV

(Submitter supplied) To identify novel targets of p63 as part of a patient-centric meta analysis, we performed RNA-sequencing on control and p63-depleted cancer cells (A253 and SCC25). In addition, we performed ChIP-sequencing analysis using multiple p63-specific antibodies, as well as antibodies targeting specific histone modifications(H3K27ac,H3K4me3 and H3K4me1) to evaluate mechanism(s) by which p63 regulates these novel targets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

25 Samples

Download data: BW, TXT

(Submitter supplied) We evaluated the gene expression changes upon the loss and gain of EHF in HNSCC cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

18 Samples

Download data: BW, TXT, XLSX

(Submitter supplied) Intratumoralmheterogeneity is a major obstacle to cancer treatment and a significant confounding factor in bulk-tumor profiling. We performed an unbiased analysis of transcriptional heterogeneity in colorectal tumors and their microenvironments using single-cell RNA–seq from 11 primary colorectal tumors and matched normal mucosa. To robustly cluster single-cell transcriptomes, we developed reference component analysis (RCA), an algorithm that substantially improves clustering accuracy. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

1220 Samples

Download data: CSV