GEO DataSets

(Submitter supplied) RNA-sequencing of RDEB SCC tumors and RDEB normal skin

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TXT

(Submitter supplied) Recessive dystrophic epidermolysis bullosa (RDEB) is a severely debilitating disorder caused by mutations in COL7A1 and is characterized by extreme skin fragility, chronic inflammation and fibrosis. A majority of RDEB patients develop squamous cell carcinoma (SCC), a highly aggressive skin cancer with limited treatment options currently available. In this study, we utilized a novel approach leveraging WGS and RNA-seq across three different tissues in a single RDEB patient to gain insight into possible mechanisms of RDEB-associated SCC progression and to identify potential novel therapeutic options. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: CSV

(Submitter supplied) The goal of this RNA-seq experiment was to determine how gene expression in RDEBSCC cell lines was altered relative to normal culture conditions when the culture media was supplemented with TGFb1 or TGFb1 and a TGFb1 inhibitor (SB431542).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

25 Samples

Download data: XLSX

(Submitter supplied) RNA-Seq was performed on 8 actinic keratoses (AK) to identify differentially expressed genes in AK vs normal skin and cutaneous squamous cell carcinoma

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) To better understand the molecular mechanisms underlying altered-FGFR3 oncogenic activity in bladder carcinomas, we made use of UMUC-14 cell lines, which endogenously expressed a mutated activated form of FGFR3 (FGFR3-S249C), the growth and transformation of these cell lines being dependent on activated-FGFR3 activity. We conducted a gene expression analysis using Affymetrix DNA arrays in this cell line treated or not with FGFR3 siRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL22321

6 Samples

Download data: CEL

(Submitter supplied) Recessive dystrophic epidermolysis bullosa (RDEB) is a monogenetic skin disorder caused by mutations in the COL7A1 gene. Missing type VII collagen leads to severe blister formation and frequent chronic wounds. Patients suffering from RDEB are prone to develop particulary aggressive squamous cell carcinoma (SCC), representing the major cause of mortality. This dataset provides Affymetrix microarray (ClariomD) based whole transcriptome data on RNA isolated from cultured primary RDEB keratinocytes (RDEB-KC) as well as RDEB squamous cell carcinoma (RDEB-SCC). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL23126

10 Samples

Download data: CEL

(Submitter supplied) Recessive dystrophic epidermolysis bullosa (RDEB) is a monogenetic skin disorder caused by mutations in the COL7A1 gene. Missing type VII collagen leads to severe blister formation and frequent chronic wounds. Patients suffering from RDEB are prone to develop particulary aggressive squamous cell carcinoma (SCC), representing the major cause of mortality. This dataset provides Affymetrix microarray (miRNA4.1) based whole transcriptome data on RNA isolated from cultured primary keratinocytes (KC) as well as squamous cell carcinoma (SCC). more...

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by array

Platform:

GPL19117

20 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL11154 GPL19699 GPL18900

108 Samples

Download data: IDAT

(Submitter supplied) Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons. Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platforms:

GPL18900 GPL19699

72 Samples

Download data: IDAT, TXT

(Submitter supplied) Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and neck cancer (HNC) tumors that predispose them to different outcomes, however this subgroup is poorly characterized due to various historical reasons. Experimental Design: we perform unsupervised gene expression clustering on well-annotated HPV(+) HNC samples from two cohorts ( 84 total primary tumors), as well as 18 HPV(-) HNCs, to discover subtypes, and begin to characterize the differences between the subtypes in terms of their HPV characteristics, pathway activity, whole-genome somatic copy number variations and mutation frequencies. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) Human tumours show a high level of clonal heterogeneity that contributes to malignant progression and metastasis, but the processes that influence the timing of metastatic dissemination of subclones are unknown. Here, we have used whole exome sequencing of 98 matched benign, malignant, and metastatic skin tumours from genetically heterogeneous mice to demonstrate that most metastases disseminate synchronously from the primary tumour, but then evolve separately, acquiring an additional set of mutations during growth at distant sites. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11533

112 Samples

Download data: CEL

(Submitter supplied) We report sequencing of 10 localized and 10 metastatic cutaneous squamous cell carcinomas from human subjects. Sequencing was done on an oncology targeted gene mutation panel consisting of 76 genes.

Organism:

Homo sapiens

Type:

Genome variation profiling by high throughput sequencing

Platform:

GPL20301

20 Samples

Download data: XLSX

(Submitter supplied) The 5-year survival rate for patients with oral squamous cell carcinomas (SCC), including tongue SCC, has not significantly improved over the last several decades. Oral potentially malignant disorders (OPMD), including oral dysplasias, are oral epithelial disorders that can develop into oral SCCs. To identify molecular characteristics that might predict conversion of OPMDs to SCCs and guide treatment plans, we performed global transcriptomic analysis of human tongue OPMD (n=9) and tongue SCC (n=11) samples with paired normal margin tissue from patients treated at Weill Cornell Medicine. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

40 Samples

Download data: TXT