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Series GSE29283 Query DataSets for GSE29283
Status Public on Dec 01, 2011
Title Pediatric Hepatocellular Carcinoma Celll Line
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Development of a new carcinoma cell line (HC-AFW1) derived from a pediatric liver tumor

The cell line HC-AFW1 was derived from a 4 year old boy suffering from HCC through culturing and passage into immuno-deficient mice. The cell line is stable now for over 8 months of culture with a doubling time of 40 h. The tumor cells show an epithelial histology and express hepatoma proteins such as Alpha-fetoprotein (AFP), Glypican 3, E-cadherin, CD10, CD326, HepPar1, Vimentin and Desmin. Catenin beta shows a deletion of 49 amino acids in the exon 3 involving the phosphorylation sites of GSK3 and is detectable in the cell nuclei. Cytogenetic analysis revealed large anomalies in the chromosomal map including chromosomal aberrations found in hepatoblastoma as well as in adult HCC.
Overall design Copy number analysis of two different passages of HC-AFW1 cells

Two tumor specimens were used for tissue culture and xenotransplantation into NSG mice. Tumor cells derived from xenografts were cultured and designated as HC-AFW1. DNA was analyzed from the passage 2 (2P2).

HC-AFW2 was derived from tissue culture without transfer in to mice. Primary tissue samples were minced into pieces of 3x3 mm and cultured on 6 well plates (Becton Dickenson, Frankfurt, Germany) in DMEM (GIBCO BRL, Carlsbad, CA) supplemented with 10% FCS (growth medium). Cell cultures were maintained in a humidified atmosphere containing 5% CO2 at 37°C. For subculturing cells were detached from the culture surface using accutase in Dulbecco´s PBS containing 0.5mM EDTA (PAA Laboratories GmbH, Cölbe, Germany) for 2-3 minutes at 37°C. A sub-cultivation ratio of 1:4 and 1:6 was performed twice per week. Cells were stored in liquid nitrogen as a suspension in complete growth medium with 10% DMSO.

DNA from patient blood and tumor samples was isolated with the QiaAmp DNA mini Kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) genotyping were performed using the Genome-Wide Human SNP Array 6.0 and Genotyping Console (GTC) software (Affymetrix, Santa Clara, CA).
Contributor(s) Armeanu-Ebinger S, Bonin M
Citation(s) 22666492
Submission date May 13, 2011
Last update date Nov 27, 2018
Contact name Michael Bonin
Organization name University Tuebingen
Department Medical Genetics
Lab Microarray Facility
Street address CAlwerstr. 7
City Tuebingen
State/province BW
ZIP/Postal code 72076
Country Germany
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (2)
GSM723813 new pediatric hepatocellular carcinoma cell line passaged from xenotransplant 2
GSM723814 new pediatric hepatocellular carcinoma cell line passaged from human tumor
BioProject PRJNA138599

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
GSE29283_RAW.tar 123.7 Mb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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