Summary from the GEO: "We report the distribution of human SATB2 in a primary zebrafish melanoma that overexpresses human SATB2, and H3K27Ac histone marks in zebrafish melanomas overexpressing either EGFP (control) or human SATB2." Overall design from the GEO: "Examining SATB2 bound regions, and H3K27Ac-bound (super) enhancers in zebrafish melanomas." Abstract summary: "Recent genomic and scRNA-seq...

Summary from the GEO: "We report gene expression data for zebrafish melanomas overexpressing human SATB2 and EGFP." Overall design from the GEO: "RNA-seq was performed on three biological replicates of primary zebrafish melanoma tumors that were excized from MCR:EGFP (control) and MCR:SATB2 overexpressing Tg(BRAF V600E);p53-/-; mitf-/- zebrafish." Abstract summary: "Recent genomic and scRNA-seq...

Summary from GEO: "Cancer cells interact with a wide variety of other cell types, but our understanding of microenvironmental heterogeneity and how it influences tumor phenotypes is limited. While single-cell RNA-seq (scRNA-seq) has helped define these TME cell types, it provides limited information on the mechanisms that define how individual tumor cells interact with TME. Here, we integrate spatial...

Summary from GEO: "We report single-cell gene expression profiling of the zebrafish melanoma cell lines ZMEL1-PRO and ZMEL1-INV under multiple in vitro and in vivo (zebrafish transplant) conditions." Overall design from GEO: "Single-cell RNA-seq of ZMEL1-PRO and ZMEL1-INV cells in one of four conditions: 1) in vitro individual culture; 2) in vitro co-culture; 3) in vivo primary tumors; and 4)...

Summary from GEO: "We report the gene expression differences between the zebrafish melanoma cell lines ZMEL1-PRO and ZMEL1-INV." Overall design from GEO: "RNA-seq of ZMEL1-PRO and ZMEL1-INV cells grown as clusters (3D) in Corning ultra-low attachment plates."

Summary from GEO: "We report how the ZMEL1-PRO cell line changes following CRISPR-Cas9 inactivation of tfap2a and tfap2e." Overall design from GEO: "RNA-seq of ZMEL1-PRO zebrafish melanoma cells following CRISPR-Cas9 with either tfap2a and tfap2e sgRNA or non-targeting control sgRNA (N=3 replicate samples each)."

Summary from GEO: "We report the gene expression differences between the zebrafish melanoma cell lines ZMEL1-PRO and ZMEL1-INV." Overall design from GEO: "RNA-seq of ZMEL1-PRO and ZMEL1-INV cells grown in standard adherent (2D) culture."

Description from Harvard Dataverse: "Deletion of caudal/cdx genes alters hox gene expression and causes defects in posterior tissues and hematopoiesis. Yet, the defects in hox gene expression only partially explain these phenotypes. To gain deeper insight into Cdx4 function, we performed ChIP-seq combined with gene expression profiling in zebrafish, and identified the transcription factor spalt-like...

Summary from GEO: "Oncogenic alterations to DNA are not transforming in all cellular contexts. This may be due to pre-existing transcriptional programs in the cell of origin. Here, we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet,...

Summary from GEO: "Broadly we were interested in understanding how fin and body melanocytes were different. The goal of the experiment was to investigate the interaction between three different variables: (1) cell lineage: melanocyte vs bulk microenvironment, (2) anatomic location: fin vs body, (3) genotype: wildtype vs CRKL,GAB2,TERT overexpression with NF1 loss. We found that melanocytes have unique...