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Series GSE94488 Query DataSets for GSE94488
Status Public on Nov 16, 2017
Title Harnessing BET inhibitor sensitivity reveals AMIGO2 as a melanoma survival gene.
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We utilize the transcriptional effects of BETi in melanoma and identify AMIGO2 as a direct target gene essential for melanoma cell survival both in vitro and in vivo. We further map the enhancer landscape of NHM and melanooma and show that genes regulated by super enhancers are expressed in higher levels, exihibit higher sensitivity to BETi, and over expressed in melanoma relative to NHM. In melanoma, AMIGO2 is regulated by super enhancers, which upon BETi lose their BRD2/BRD4 enrichment, resulting in AMIGO2 silencing.
Overall design We interogate two NHM culures and four melanoma cell lines for transcriptional changes upon BET inhibition and correlate those wiith changes in enhancer landscape and BRD2/4 occupancy at regulatory regions.
Contributor(s) Fontanals-Cirera B, Hasson D, Vardabasso C, Hernando E, Bernstein E
Citation(s) 29149598
Submission date Feb 03, 2017
Last update date May 15, 2019
Contact name Emily Bernstein
Phone (212) 824-9335
Organization name Mount Sinai School of Medicine
Department Oncological Sciences
Lab Bernstein Lab
Street address 1470 Madison Avenue, 6th floor Rm 302
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (69)
GSM2476338 Normal Human Melanocytes ATAC-seq [NHM1]
GSM2476339 NRAS metastatic melanoma ATAC-seq [SKmel147]
GSM2476340 BRAF metastatic melanoma ATAC-seq [501MEL]
BioProject PRJNA369853
SRA SRP098821

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE94488_501MEL-RNA-AMIGO2KD-gene_exp.diff.gz 930.4 Kb (ftp)(http) DIFF
GSE94488_501MEL-RNA-JQ1-gene_exp.diff.gz 5.7 Mb (ftp)(http) DIFF
GSE94488_RAW.tar 9.5 Gb (http)(custom) TAR (of BW)
GSE94488_RNA-gene_exp.diff.gz 34.0 Mb (ftp)(http) DIFF
GSE94488_SKmel147-RNA-AMIGO2KD-gene_exp.diff.gz 918.7 Kb (ftp)(http) DIFF
GSE94488_SKmel147-RNA-JQ1-gene_exp.diff.gz 5.8 Mb (ftp)(http) DIFF
GSE94488_Titels_in_diff_files.xlsx.gz 39.2 Kb (ftp)(http) XLSX
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Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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