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Sample GSM755614 Query DataSets for GSM755614
Status Public on Jul 01, 2014
Title peripheral blood 4.20
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics tumor stage: not applicable
gender: Female
tissue: Blood
disease state: carcinoma
Extracted molecule genomic DNA
Extraction protocol Extraction of genomic DNA was done using a BioRobot M48 Workstation with MagAttract technology (Qiagen)
Label A-DNP, C-Bio
Label protocol 200 ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).
 
Hybridization protocol RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).
Scan protocol After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
Description Genomic DNA extracted from peripheral blood was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
Data processing Genomic DNA extracted from clear cell renal cell carcinoma was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChips (Illumina).
 
Submission date Jul 06, 2011
Last update date Jul 01, 2014
Contact name Linda Köhn
E-mail(s) linda.kohn@medbio.umu.se
Phone +46907852873
Organization name Umeå University
Department Medical Biosciences/pathology
Street address Building 6M
City Umeå
ZIP/Postal code 90185
Country Sweden
 
Platform ID GPL13829
Series (1)
GSE30460 Genomic aberrations predicts survival in clear cell renal cell carcinoma

Data table header descriptions
ID_REF
VALUE Image data was analyzed using Beadstudio 3.1.3.0 with GT module 3.2.33 (Illumina) and Genomestudion 2010.3 with GT module 1.8.4.
GC_Score
Theta
R
B Allele Freq
Log R Ratio

Data table
ID_REF VALUE GC_Score Theta R B Allele Freq Log R Ratio
cnvi0111185 NC 0 0.970071 1.698145 0.9949803 0.2245451
cnvi0111186 NC 0 0.03495884 0.60325 0.005140681 0.2765916
cnvi0111187 NC 0 0.9766326 1.574333 0.9911357 0.0431246
cnvi0111188 NC 0 0.0131655 1.155682 0 -0.1753205
cnvi0111189 NC 0 0.03274551 1.327772 0.006741865 -0.1193037
cnvi0111190 NC 0 0.01490311 0.4450105 0 0.3107097
cnvi0111191 NC 0 0.0319261 1.375155 0.003450371 0.3227627
cnvi0111192 NC 0 0.04074975 1.101783 0.01481693 -0.01581921
cnvi0111193 NC 0 0.018178 1.300771 0.004554469 0.09954365
cnvi0111194 NC 0 0.9632206 1.114953 0.9794627 -0.2552119
cnvi0111195 NC 0 0.0386949 1.901509 0.006509961 -0.03824696
cnvi0111196 NC 0 0.9712255 1.200452 0.9873564 -0.03213269
cnvi0111197 NC 0 0.002555898 0.8055576 0 -0.1481455
cnvi0111198 NC 0 0.9573433 1.392103 0.9860841 0.1020441
cnvi0111199 NC 0 0.01964112 1.281308 0.002281401 0.0110583
cnvi0111200 NC 0 0.9773 0.7522057 0.9928219 -0.2296061
cnvi0111201 NC 0 0.05057835 0.9590177 0.03357036 0.05223934
cnvi0111202 NC 0 0.8959519 1.431367 0.9671231 0.1025031
cnvi0111203 NC 0 0.04848 1.745883 0.02475037 0.07552224
cnvi0111204 NC 0 0.9851596 1.246689 0.9966097 0.03312587

Total number of rows: 299140

Table truncated, full table size 18228 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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