GEO DataSets

(Submitter supplied) To understand the diversity of expression states within melanoma tumors, we obtained freshly resected samples, dissagregated the samples, sorted into single cells and profiled them by single-cell RNA-seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4645 Samples

Download data: TXT

(Submitter supplied) RNA-seq of pre-treatment and post-relapse matched samples from melanoma patients

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: XLSX

(Submitter supplied) We subjected 196 melanoma tumors to genome-wide methylation analysis using the Illumina Infinium MethylationEPIC BeadChip array.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL21145

196 Samples

Download data: TXT, XLSX

(Submitter supplied) The primary cause of cancer deaths is metastasis. While studies have identified multiple signals that drive invasiveness, the first step in metastatic colonisation, the reason for cells to move away from the primary tumor is less well understood. Salubrinal inhibits an eIF2-alpha phosphatase and consequently leads to increase eIF2-alpha phosphorylation and inhibition of the eIF2B translation initiation factor, leading to reprogramming of translation. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

15 Samples

Download data: TXT

(Submitter supplied) The primary cause of cancer deaths is metastasis. While studies have identified multiple signals that drive invasiveness, the first step in metastatic colonization, the reason for cells to move away from the primary tumor is less well understood. The dataset presented here examines the effect of different culture conditions on gene expression by comparing expression of a melanoma cell line in nutrient rich DMEM to MEM. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) Adoptive cell therapies (ACT) with cytotoxic T-cell targeting melanocytic antigens can achieve remissions in metastatic melanoma patients, but tumours frequently relapse. To study the underlying mechanisms of resistance we have generated a genetically engineered mouse melanoma model that faithfully recapitulates tumour regression, remission and relapse as seen in patients. HCmel3 mouse melanoma cells were injected into syngneic C57/BL6 (H-2b) mice. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

21 Samples

Download data: TXT

(Submitter supplied) A panel of 29 melanoma cell lines were gene expression profiled by RNA-Seq.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

29 Samples

Download data: TXT

(Submitter supplied) Increased MITF expression contributes to melanoma progression and resistance to BRAF pathway inhibition. We show that, unexpectedly, lack of MITF is associated with more severe resistance to a range of inhibitors. Indeed, the presence of endogenous MITF was essential for robust drug responses. Both in primary and acquired resistance, MITF levels inversely correlated with expression of several activated receptor tyrosine kinases, most commonly AXL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

14 Samples

Download data: TXT

(Submitter supplied) Homeostatic programs maintain equilibrium between immune protection, and selftolerance. Such mechanisms impact autoimmunity and tumor formation, respectively. How tissue homeostasis is maintained, and impacts tumor surveillance is unknown. Here we identify that mononuclear phagocytes share conserved programming during homeostatic differentiation, and entry into tissue. IFNγ is necessary and sufficient to induce these transcripts, revealing a key instructive role. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

333 Samples

Download data: TXT

(Submitter supplied) Homeostatic programs maintain equilibrium between immune protection, and selftolerance. Such mechanisms impact autoimmunity and tumor formation, respectively. How tissue homeostasis is maintained, and impacts tumor surveillance is unknown. Here we identify that mononuclear phagocytes share conserved programming during homeostatic differentiation, and entry into tissue. IFNγ is necessary and sufficient to induce these transcripts, revealing a key instructive role. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Homeostatic programs maintain equilibrium between immune protection, and selftolerance. Such mechanisms impact autoimmunity and tumor formation, respectively. How tissue homeostasis is maintained, and impacts tumor surveillance is unknown. Here we identify that mononuclear phagocytes share conserved programming during homeostatic differentiation, and entry into tissue. IFNγ is necessary and sufficient to induce these transcripts, revealing a key instructive role. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

9 Samples

Download data: CEL

(Submitter supplied) Purpose: The heterogeneity of tumor cells presents a major challenge to cancer diagnosis and therapy. Cutaneous T cell lymphomas (CTCL) are a group of T lymphocyte malignanciesthat primarily affect skin. Lack of highly specific markers for malignant lymphocytes prevents early diagnosis, while only limited treatment options are available for patients with advanced-stage CTCL.Droplet-basedsingle-cell transcriptome analysis of CTCL skin biopsiesopens avenues for dissecting patient-specificT lymphocyte heterogeneity, providing a basis for identifying specific markers for diagnosis and cure of CTCL. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: CSV

(Submitter supplied) Panel of 53 melanoma cell lines were gene expression profiled by RNA-Seq for molecular classification

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

53 Samples

Download data: TXT

(Submitter supplied) Malignant melanoma is an aggressive cancer known for its notorious resistance to most current therapies. The basic helix-loop-helix microphthalmia transcription factor (MITF) is the master regulator determining the identity and properties of the melanocyte lineage, and is regarded as a lineage-specific ‘oncogene’ that has a critical role in the pathogenesis of melanoma. MITF promotes melanoma cell proliferation, whereas sustained supression of MITF expression leads to senescence. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: BED

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL20301 GPL18573

337 Samples

Download data: MTX, TSV

(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from 10x Genomics platform was analyzed to dissect this problem at multiple scales. Data indicates that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: MTX, TSV

(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the SMART-seq/Fluidigm and 10x Genomics platforms were analyzed to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

327 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to apply the SAKE algorithms to identify drug-resistant cellular populations as human melanoma cells respond to targeted BRAF inhibitors. Single-cell RNA-Seq data from both the SMART-seq/Fluidigm and 10x Genomics platforms were analyzed to dissect this problem at multiple scales. Data from both platforms indicate that BRAF inhibitor resistant cells can emerge from rare populations already present before drug application, with SAKE identifying both novel and known markers of resistance

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Uveal melanoma (UM) is a highly metastatic cancer that, in contrast to cutaneous melanoma, is largely unresponsive to checkpoint immunotherapy. In this study we interrogate the tumour microenvironment at single-cell resolution using scRNA-seq of 59,915 tumour and non-neoplastic cells from 8 primary and 3 metastatic samples. A subset analysis of tumour cells confirms the global genomic landscape established from bulk analysis and reveals newly described subclonal genomic complexity and transcriptional states consistent with phenotype plasticity. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24268

11 Samples

Download data: MTX, TSV

(Submitter supplied) The X-linked DDX3X gene encodes an ATP-dependent DEAD-box RNA helicase frequently altered in various human cancers including melanomas. Despite its important roles in translation and splicing, how DDX3X dysfunction specifically rewires gene expression in melanoma remains completely unknown. Here we uncover a DDX3X-driven post-transcriptional program that dictates melanoma phenotype and poor disease prognosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: TXT