Fresh tumor tissues for engraftment were placed in ice-chilled high glucose DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 U/mL streptomycin and rapidly processed for engraftment. After removing necrotic tissue and washing three times in ice-cold PBS, tumor specimens were divided under aseptic sterile conditions using a No.10 scalpel blade to yield 2 × 1 × 1 mm3 pieces. The tissue fragments were then incubated in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 100 U/mL streptomycin (condition 1), or in DMEM medium supplemented with 50% Matrigel™ (BD; 356234), 10 ng/mL epidermal growth factor (Gibco; PHG0314), 10 ng/ml basic fibroblast growth factor (Gibco; PHG0264), 100 U/mL penicillin, and 100 U/mL streptomycin (condition 2) for 30 min. After sterilizing the dorsal shaved area(s) with Betadine® surgical scrub, followed by 70% ethanol, three or four pieces of tissue were transplanted subcutaneously into the right flanks of NOD/SCID mice (n = 3) with a No.2 trocar.
Extracted molecule
genomic DNA
Extraction protocol
DNA from each sample was digested using the NspI (Cat#R0602L, New England BioLabs, Ipswich, MA, US) and StyI (Cat#R0500L, New England BioLabs) restriction enzymes, and two adaptors were ligated to the DNA fragment for PCR amplification. To obtain biotin-labeled DNA, amplified DNA was labeled using the Affymetrix® Genome-Wide Human SNP Nsp/Sty Assay Kit 6.0 (Cat#901015, Affymetrix, Santa Clara, CA, US) according to the manufacturer’s instructions.
Label
biotin
Label protocol
Affymetrix protocol
Hybridization protocol
Affymetrix protocol
Scan protocol
Affymetrix protocol
Description
genotyping data from PDX19 F3
Data processing
The CEL files wrere read by R function crlmm. I only keep SNP probes (906600), and removed probes whose chromosomes are "NA". Therefore, the Sample table contains 905422 rows.
