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Series GSE180665 Query DataSets for GSE180665
Status Public on Jul 29, 2021
Title Modeling Hepatoblastoma: Identification of Distinct Tumor Cell Populations and Key Genetic Mechanisms through Single Cell Sequencing (scRNA-seq)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Hepatoblastoma (HB) is the most common primary liver malignancy of childhood. However, molecular investigations of the disease are limited and effective treatment options are lacking. The use of patient derived xenografts (PDX) to study biology and treatment strategies of HB has proven to be a useful tool. There is currently a knowledge gap in the investigation of key driver cells of HB in PDX models. Key driving pathways of HB tumor including WNT, AP-1, Hedgehog, Notch and MAPK pathways and genes such as GPC3, DLK1 and HMGA2 have been identified in primary HB tumor and PDX as integral players in HB tumor growth. Cell clusters have been defined with distinct roles in tumor development. Cell populations with initiating, angiogenic (endothelial), maintenance, and progression signatures have been identified in one HB patient tumor and corresponding PDX tumor. Critical pathways combined with identification of distinct cell populations within HB tumor will allow for investigation of novel treatment strategies in vitro and in vivo.
 
Overall design To examine HB pathways and define cell populations in a heterotopic PDX model, we implant patient source tumor into the intrascapular fat pad of female NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice. PDX tumor was compared to background liver and primary HB tumor and evaluated using single cell RNA sequencing (scRNAseq). 26,886 cells across 3 samples were collected after preprocessing and quality control.
 
Contributor(s) Bondoc A, Glaser K, Jin K, Lake C, Cairo S, Geller J, Tiao G, Aronow B
Citation(s)
  • Bondoc A, Glaser K, Jin K, Lake C et al. Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma. Commun Biol 2021 Sep 8;4(1):1049. PMID: 34497364
Submission date Jul 22, 2021
Last update date Sep 29, 2021
Contact name Bruce J Aronow
E-mail(s) bruce.aronow@cchmc.org
Organization name Cincinnati Children's Hospital Medical Center
Department Biomedical Informatics, Developmental Biology
Lab Genome Informatics
Street address 240 Albert Sabin Way
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (7)
GSM5467406 HB 17 Background
GSM5467407 HB 17 Hepatoblastoma
GSM5467408 HB 17 PDX
This SubSeries is part of SuperSeries:
GSE180666 Modeling Hepatoblastoma
Relations
BioProject PRJNA749050
SRA SRP329506

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
GSE180665_Cell_metadata_after_integration.xlsx 4.9 Mb (ftp)(http) XLSX
GSE180665_RAW.tar 2.6 Gb (http)(custom) TAR (of TAR)
GSE180665_hb_integrated_normalized_annotated_harmony.h5ad.gz 387.6 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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