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Sample GSM2409924 Query DataSets for GSM2409924
Status Public on Dec 01, 2016
Title HMP359-F2
Sample type genomic
 
Source name PDX40-F2
Organism Homo sapiens
Characteristics tissue: liver
Growth protocol 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 PDX40 F2
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.
 
Submission date Nov 29, 2016
Last update date Dec 01, 2016
Contact name hong li
E-mail(s) lihong01@sibs.ac.cn
Organization name SIBS
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL6801
Series (2)
GSE90651 SNP data from hepatocellular carcinoma PDX
GSE90653 Data from hepatocellular carcinoma PDX

Data table header descriptions
ID_REF
VALUE genotype calls are represented by 1 (AA), 2 (AB) and 3 (BB).

Data table
ID_REF VALUE
SNP_A-2131660 AA
SNP_A-1967418 BB
SNP_A-1969580 BB
SNP_A-4263484 AA
SNP_A-1978185 AA
SNP_A-4264431 AB
SNP_A-1980898 BB
SNP_A-1983139 AA
SNP_A-4265735 AA
SNP_A-1995832 BB
SNP_A-1995893 BB
SNP_A-1997689 BB
SNP_A-1997709 AA
SNP_A-1997896 AA
SNP_A-1997922 AB
SNP_A-2000230 AA
SNP_A-2000332 AA
SNP_A-2000337 AA
SNP_A-2000342 AA
SNP_A-4268173 AA

Total number of rows: 905422

Table truncated, full table size 15031 Kbytes.




Supplementary file Size Download File type/resource
GSM2409924_BHP2013047-15_PDX40-F2_GenomeWideSNP_6_.CEL.gz 27.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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