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Series GSE74230 Query DataSets for GSE74230
Status Public on Jan 15, 2018
Title Positively selected enhancer elements endow tumor cells with metastatic competence
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in signature enhancer-histone marks between near-isogenic pairs of high and low lung-metastatic osteosarcoma cells. We term these regions Metastatic Variant Enhancer Loci (Met-VELs). Met-VELs drive coordinated waves of gene expression during metastatic colonization of the lung. Met-VELs cluster non-randomly, indicating that activity of these enhancers and their associated gene targets is positively selected. Osteosarcoma lung metastasis is inhibited by global interruptions of Met-VEL associated gene expression.
 
Overall design Examination of H3K4me1, H3K27ac, and Dnase I Hypersensitivity data in highly and non-metastatic osteosarcoma cell line pairs (n=5 pairs) as well as primary and metastatic tumors in human patients (n=5 pairs). Global gene expression during metastatic progression in ex vivo model of lung metastasis was also examined for 3 cell line pairs.
 
Contributor(s) Morrow JJ, Saiakhova AR, Scacheri PC
Citation(s) 29334376
Submission date Oct 21, 2015
Last update date May 15, 2019
Contact name Peter Scacheri
E-mail(s) pxs183@case.edu
Phone 216-368-3458
Organization name Case Western Reserve University
Street address 10900 Euclid Ave; BRB 647
City Cleveland Heights
State/province OH
ZIP/Postal code 44106
Country USA
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (91)
GSM1914980 143B: Dnase I Hypersensitivity
GSM1914981 143B: H3K27ac ChIP Seq
GSM1914982 143B: H3K4me1 ChIP Seq
Relations
BioProject PRJNA299597
SRA SRP065191

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
GSE74230_RAW.tar 16.3 Gb (http)(custom) TAR (of BED, BW, TXT)
GSE74230_adapters.txt.gz 761 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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