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Sample GSM775142 Query DataSets for GSM775142
Status Public on Aug 09, 2014
Title A31
Sample type genomic
 
Source name gDNA from whole blood
Organism Homo sapiens
Characteristics sample id: A31
gender: M
total cholesterol (tc): 258
triglycerides (tg): 356
ldl: 71.00
percent stenosis: >50%
admin note: CAD-II
Treatment protocol None
Growth protocol None
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from whole blood using the Gentra Puregene Blood Kit (Qiagen). DNA quality and quantity was assessed using a Nanodrop Spectrophotometer ND-1000.
Label biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing CEL files and CHP files (generated by Affymetrix GTC 4.0 using the birdseed V2 algorithm). CNV analysis was generated by PARTEK Genomic Suite 6.5 using genomic segmentation algorithm (CN5) by default parameters (CNCHP files).
 
Submission date Aug 09, 2011
Last update date Aug 09, 2014
Contact name Wei-Chung Shia
Organization name Changhua Christian Hospital
Department Cancer Research Center
Street address 8F., No.235, Xuguang Rd.
City Changhua City
ZIP/Postal code 500
Country Taiwan
 
Platform ID GPL6801
Series (1)
GSE31276 Genetic Copy Number Variants in Myocardial Infarction Patients with Hyperlipidemia

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 1.000000 1 51586 -0.294423 1.238438 nan nan
CN_473964 1.000000 1 51659 -0.354781 1.238430 nan nan
CN_473965 1.000000 1 51674 -0.500100 1.238428 nan nan
CN_473981 1.000000 1 52771 -0.191178 1.238304 nan nan
CN_473982 1.000000 1 52788 -0.635494 1.238302 nan nan
CN_497981 1.000000 1 62627 -0.198474 1.237141 nan nan
CN_502615 1.000000 1 75787 -0.048182 1.235457 nan nan
CN_502613 1.000000 1 75849 -0.095203 1.235448 nan nan
CN_502614 1.000000 1 76175 -0.700256 1.235405 nan nan
CN_502616 1.000000 1 76192 -0.834000 1.235403 nan nan
CN_502843 1.000000 1 88453 -0.412285 1.233705 nan nan
CN_466171 1.000000 1 218557 -0.547428 1.416062 nan nan
CN_468414 1.000000 1 218926 -0.581114 1.416094 nan nan
CN_468412 1.000000 1 219009 0.032214 1.416101 nan nan
CN_468413 1.000000 1 219024 -0.281889 1.416103 nan nan
CN_470565 1.000000 1 219470 -0.113628 1.416142 nan nan
CN_468424 1.000000 1 225521 -0.015562 1.416670 nan nan
CN_468425 1.000000 1 225579 -0.440867 1.416675 nan nan
CN_460512 1.000000 1 346294 -0.651889 1.328164 nan nan
CN_460513 1.000000 1 346393 -0.007811 1.328165 nan nan

Total number of rows: 1813441

Table truncated, full table size 114238 Kbytes.




Supplementary file Size Download File type/resource
GSM775142_A31.CEL.gz 31.6 Mb (ftp)(http) CEL
GSM775142_A31.CN5.CNCHP.gz 34.8 Mb (ftp)(http) CNCHP
GSM775142_A31.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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