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Sample GSM2768929 Query DataSets for GSM2768929
Status Public on Aug 31, 2017
Title Patient Derived Xenograft Serial Passage 0
Sample type genomic
Source name Xenograft
Organism Homo sapiens
Characteristics host strain: NOD/SCID mouse
tissue/cell type: Patient-derived xenograft
passage: passage 0
Growth protocol Tumor growth was established in NOD/SCID mouse and tumors have been passaged serially
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from tumor samples snap frozen in liquid nitrogen at the time of passaging. We used a Proteinase K/SDS buffer to dissociate the tissue (10 mM Tris-Cl (pH 8.0), 0.1 M EDTA (pH 8,0), 0.5% (w/v) SDS, 20mg/mL Proteinase K) overnight at 55°C. Protein extraction was achieved with Phenol-Chloroform-Isoamyl alcohol using phase lock centrifuge gels (5-Prime, Gaithersburg, USA) and DNA was precipitated with 100% ethanol and 7.5 M ammonium acetate. The pellet was washed with 75% ethanol and then dried.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
Hybridization protocol Standard Affymetrix procedures
Scan protocol Standard Affymetrix procedures
Description PDX0
Data processing Data was imported into Partek Genomic Suite using Partek defaults as allele specific intensity which was converted to copy number.
Submission date Aug 31, 2017
Last update date Jan 23, 2018
Contact name Marc Remke
Organization name German Cancer Research Center (DKFZ)
Department Pediatric Neuro-Oncogenomics
Street address Moorenstr. 5
City Düsseldorf
State/province NRW
ZIP/Postal code 40225
Country Germany
Platform ID GPL6801
Series (1)
GSE103342 Characterization of a clival chordoma xenograft model reveals inherent tumor genomic instability

Data table header descriptions
VALUE Copy number

Data table
AFFX-SNP_10000979 3.64941
AFFX-SNP_10009702 1.99457
AFFX-SNP_10015773 2.36788
AFFX-SNP_10021569 3.4984
AFFX-SNP_10026879 1.65033
AFFX-SNP_10029725 2.0398
AFFX-SNP_10034687 3.00006
AFFX-SNP_10036267 2.04798
AFFX-SNP_10037362 1.76904
AFFX-SNP_10037636 1.66553
AFFX-SNP_10039349 1.24485
AFFX-SNP_10039442 2.17462
AFFX-SNP_10039933 1.74229
AFFX-SNP_10046830 1.66429
AFFX-SNP_10047363 2.82882
AFFX-SNP_10047841 8.36848
AFFX-SNP_10049334 0.94776
AFFX-SNP_10052664 5.15541
AFFX-SNP_10057887 1.33922
AFFX-SNP_10064911 3.27962

Total number of rows: 1855448

Table truncated, full table size 36515 Kbytes.

Supplementary file Size Download File type/resource
GSM2768929_GW6_040816W_JR02_PDX0.CEL.gz 26.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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