GEO DataSets

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

Organism:

Homo sapiens; Danio rerio

Type:

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

4 related Platforms

37 Samples

Download data: PAIR, XLS

(Submitter supplied) We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14607

8 Samples

Download data: PAIR

(Submitter supplied) We report the gene expression comparison of human A375 melanoma cells with GDF6 and BMP pathway modulation. These comparisons were used to determine the gene signature regulated by GDF6.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: XLS

(Submitter supplied) We report the gene expression comparison of zebrafish melanocytes and melanomas. These comparisons were used for integrative genomic studies that identified the BMP factor GDF6 as a new oncogene that is specifically expressed in melanomas.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

8 Samples

Download data: XLS

(Submitter supplied) We report the gene expression comparison of human A375 melanoma cells with GDF6 and BMP pathway modulation. These comparisons were used to determine the gene signature regulated by GDF6.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: TXT

(Submitter supplied) Neuregulin (NRG) signaling through the receptor tyrosine kinase, ERBB3, is required for embryonic development, and dysregulated signaling has been associated with cancer progression. Here, we show that NRG1/ERBB3 signaling inhibits melanocyte (MC) maturation and promotes undifferentiated, migratory and proliferative cellular characteristics. Embryonic analyses demonstrated that initial MC specification and distribution were not dependent on ERBB3 signaling. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

6 Samples

Download data: CEL, CHP

(Submitter supplied) To determine the role of PRL3 in gene regulation, empty vector or HA-tagged PRL3 was stably expressed in cultured human melanoma A375 cells. ChIP-seq was used to determine the impact of increased PRL3 expression on the genome-wide distribution of RNA Polymerase II (Total/Ser5-Phosphorylated/Ser2-Phosphorylated), MITF and DDX21. In combination with transcriptional analysis (4sU-seq; GEO accession - GSE127855), this study demonstrated that PRL3 overexpression leads to reduced RNA polymerase processivity at a subset of so called 'restricted' genes which are enriched for endolysosomal functions.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21697

32 Samples

Download data: BIGWIG

(Submitter supplied) We report the use of 4sU-seq to determine the role of PRL3 in transcriptional processivity in human melanoma cells overexpressing either PRL3 or empty vector control. Genome-wide analysis of read coverage across length of equalised genes revealed a distinct accumulation of transcripts towards the 5’ end in PRL3 overexpressing cells. Furthermore, we identify the genes that were enriched with 5’ transcripts in the PRL3 expressing cells by comparing the intronic read counts (normalized for length) at the 5’ and 3’ end of the gene and termed this metric the transcriptional processivity ratio (TPR). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Through recurrent bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate into pigment-producing melanocytes. The signaling factors orchestrating these events remain incompletely understood. Here, we use single cell RNA-sequencing with comparative gene expression analysis to elucidate the transcriptional dynamics of McSCs through quiescence, activation, and melanocyte maturation. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: BW, NARROWPEAK

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL21103 GPL19057

1815 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Adult tissue stem cells protect their long-term potential by exerting precise control over their transitions between quiescence, activation, and differentiation. Through cyclic bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate to produce and transfer pigment to hair cells.  The signaling factors orchestrating this process are still poorly understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1804 Samples

Download data: CSV

(Submitter supplied) Adult tissue stem cells protect their long-term potential by exerting precise control over their transitions between quiescence, activation, and differentiation. Through cyclic bouts synchronous with the hair cycle, quiescent melanocyte stem cells (McSCs) become activated to generate proliferative progeny that differentiate to produce and transfer pigment to hair cells.  The signaling factors orchestrating this process are still poorly understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

5 Samples

Download data: TXT

(Submitter supplied) We have used lentiviral shRNA vectors to generate pools of melanoma cells (1205Lu and WM9) stably knocked down for ILEI (FAM3C).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

18 Samples

Download data: CEL

(Submitter supplied) MIcrophthalmia-associated Transcription Factor (MITF) regulates melanocyte and melanoma physiology. ShRNA-mediated silencing of the NURF subunit BPTF revealed its essential role in several melanoma cell lines and in untransformed melanocytes in vitro. Comparative RNA-seq shows that MITF and BPTF co-regulate overlapping gene expression programs in cell lines in vitro. Somatic and specific inactivation of Bptf in developing murine melanoblasts in vivo shows that Bptf regulates their proliferation, migration and morphology. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: TXT

(Submitter supplied) To discover potential biomarkers of melanoma development and progression, we embarked on studies comparing the glycomic gene profiles of normal human epidermal melanocytes with human metastatic melanoma (MM) cells represented by A375 and G361 cell lines. Glycomic features embody all of those enzymatic, membranous and regulatory proteins that influence glycan ‘sugar’ formation/degradation on a cell. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11097

6 Samples

Download data: CEL