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Sample GSM1408469 Query DataSets for GSM1408469
Status Public on Jun 11, 2014
Title Blood_1_778
Sample type genomic
 
Source name peripheral blood leukocytes_case
Organism Homo sapiens
Characteristics group: gastric cancer case
gender: male
Treatment protocol The isolated samples are stored in -80deg C deep freezer.
Growth protocol Peripheral blood drawn from venous was stored in an icebox after obtaining to keep cool and was centrifused within one hour. After discarding supernatant, the blood was isolated as serum, plasma, RBC, whole blood, and buffy coat and stored in cryotube.
Extracted molecule genomic DNA
Extraction protocol After the blood samples are thawed, standard citrate buffer is added, mixed, and the tubes are centrifuged and the top portion of the supernatant is discarded (twice). The pellet is resuspended in a solution of SDS detergent and proteinase K, and the mixture is incubated at 55deg C for one hour. The sample then is phenol extracted once with a phenol/chloroform/isoamyl alcohol solution, and after centrifugation the aqueous layer is removed to a fresh microcentrifuge tube. The DNA is ethanol precipitated, resuspended in buffer, and then ethanol precipitated a second time. Once the pellet is dried, buffer is added and the DNA is resuspended by incubation.
Label Biotin
Label protocol About 200ng of genomic DNA is amplified and randomly fragmented into 25 to 125 base pair (bp) fragments. gDNA initial amplification reacted in 40㎕ reaction volume, containing 20㎕ volume of genomic DNA at a concentration of 10ng/㎕, 20㎕ of Denaturation Master Mix. The reaction of initial amplification carried out as follows: 10min at Room Temperature. After the initial amplification, the incubated products were amplicated with 130㎕ of Axiom 2.0 Neutral Soln, 225㎕ Axiom 2.0 Amp Soln and 5㎕ Axiom 2.0 Amp Enzyme. The amplification reactions were carried out as follows: 23hour ± 1hour at 37℃. The amplification products were performed in optimized reaction to amplify fragments between 200-1,100 base pairs. A fragmentation step then reduced the amplified products to segments of approximately 25-50 bp, which were then end-labeled using biotinylated nucleotides.
 
Hybridization protocol Following hybridization, the bound target is washed under stringent conditions to remove non-specific background to minimize background noise caused by random ligation events. Each polymorphic nucleotide is queried via a multi-color ligation event carried out on the array surface.
Scan protocol After ligation, the arrays are stained and imaged on the GeneTitan MC Instrument (Affymetrix, Santa Clara, CA, USA)
Description Hybridized to Axiom®_Exome_319
Data processing Using rawdata(cel files) as input, data analysis was conducted by Affymetrix power tools(APT) in linux server. APT-probeset-gneotype program, one of the APT applications, was used to gain genotype call as well as CHP files, which was run by birdseed-v2 algorithm as analysis option.
 
Submission date Jun 10, 2014
Last update date Jun 11, 2014
Contact name Boyoung Park
Organization name National Cancer Centerm Korea
Street address 323 Ilsan-ro, Ilsandong-gu, Goyang-si
City Gyeonggi-do
ZIP/Postal code 410-769
Country South Korea
 
Platform ID GPL18760
Series (1)
GSE58356 Axiom® Exome 319 Array data to identify susceptible genetic variations of gastric cancer

Data table header descriptions
ID_REF PROBE SET NAME
VALUE Genotype Call: AA = 0, AB = 1, BB = 2, NN = -1
CONFIDENCE
FORCED CALL

Data table
ID_REF VALUE CONFIDENCE FORCED CALL
AFFX-KIT-000001 AA 0.000010 AA
AFFX-KIT-000002 AA 0.000002 AA
AFFX-KIT-000003 AA 0.000002 AA
AFFX-KIT-000004 AB 0.000004 AB
AFFX-KIT-000005 AA 0.000026 AA
AFFX-KIT-000008 AA 0.000309 AA
AFFX-KIT-000009 AB 0.000021 AB
AFFX-KIT-000012 AA 0.000107 AA
AFFX-KIT-000013 AA 0.000003 AA
AFFX-KIT-000014 BB 0.000020 BB
AFFX-KIT-000015 BB 0.000003 BB
AFFX-KIT-000016 AB 0.000011 AB
AFFX-KIT-000017 AA 0.000007 AA
AFFX-KIT-000018 BB 0.000018 BB
AFFX-KIT-000019 BB 0.000014 BB
AFFX-KIT-000021 AA 0.000009 AA
AFFX-KIT-000022 BB 0.000017 BB
AFFX-KIT-000023 AB 0.000009 AB
AFFX-KIT-000025 AB 0.000008 AB
AFFX-KIT-000026 BB 0.000008 BB

Total number of rows: 319283

Table truncated, full table size 8419 Kbytes.




Supplementary file Size Download File type/resource
GSM1408469_Axiom_Exome319_13-12_KJS778_A10.AxiomGT1.chp.gz 4.7 Mb (ftp)(http) CHP
GSM1408469_Axiom_Exome319_13-12_KJS778_A10.CEL.gz 7.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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