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Series GSE150705 Query DataSets for GSE150705
Status Public on May 19, 2020
Title Genome-wide analysis of hemangiosarcoma tumor tissue using ChRO-seq finds ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis.
Organism Canis lupus familiaris
Experiment type Other
Summary Canine hemangiosarcoma (HSA) is an aggressive vascular tumor that arise from malignant endothelial cells. To gain deeper understanding of HSA pathogenesis, we performed Chromatin-Run-On sequencing (ChRO-seq) experiment on 17 HSA tumor tissues and 4 normal tissue. ChRO-seq analysis revealed over a thousand differentially expressed genes in HSA tissue compared with normal splenic tissue (FDR <0.005). Interestingly the majority of genes overexpressed in HSA tumor tissue were associated with extracellular matrix (ECM) remodeling. This observation correlated well with our histological analysis, which found that HSA tumors contain a rich and complex collagen network. Additionally, we characterized the protein expression patterns of two highly overexpressed molecules identified in ChRO-seq analysis, podoplanin (PDPN) and laminin alpha 4 (LAMA4). We found that the expression of these two ECM-associated factors appeared to be largely limited to transformed endothelial cells within the HSA lesions. Outcomes from this study suggest that ECM remodeling has an important role in HSA pathogenesis.
Overall design ChRO-seq was used to analyze canine splenic hemangiosarcoma tissues and normal splenic tissues.
Contributor(s) Mukai C, Danko CG, Coonrod SA
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Submission date May 16, 2020
Last update date May 21, 2020
Contact name Scott Coonrod
Organization name Cornell University
Department Baker Institute for Animal Health
Lab Coonrod lab
Street address 235 Hungerford Hill Road
City Ithaca
State/province New York
ZIP/Postal code 14853
Country USA
Platforms (1)
GPL21400 Illumina NextSeq 500 (Canis lupus familiaris)
Samples (21)
GSM4556970 canine tissue from B775
GSM4556971 canine tissue from B297NM
GSM4556972 canine tissue from B307NM
BioProject PRJNA633277
SRA SRP261959

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Supplementary file Size Download File type/resource
GSE150705_RAW.tar 1.4 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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