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Sample GSM755628 Query DataSets for GSM755628
Status Public on Jul 01, 2014
Title peripheral blood 6.41
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics tumor stage: not applicable
gender: Male
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 0.9765932 1.383905 1 -0.07066943
cnvi0111186 NC 0 0.02022048 0.603833 0 0.2779852
cnvi0111187 NC 0 0.9751623 1.586607 0.9896049 0.05432891
cnvi0111188 NC 0 0.02177556 1.231498 0.007318942 -0.0836508
cnvi0111189 NC 0 0.03711935 1.351616 0.01134923 -0.0936259
cnvi0111190 NC 0 0.05686195 0.5326267 0.02128894 0.569995
cnvi0111191 NC 0 0.04160795 1.264031 0.01367346 0.2012008
cnvi0111192 NC 0 0.04993009 1.118787 0.02449084 0.00627625
cnvi0111193 NC 0 0.02085327 1.252545 0.007336736 0.04503855
cnvi0111194 NC 0 0.9816986 1.332913 0.9987442 0.002387894
cnvi0111195 NC 0 0.0499845 1.843623 0.01847868 -0.08284812
cnvi0111196 NC 0 0.980176 1.367966 0.9966918 0.1563224
cnvi0111197 NC 0 0.008341073 1.001379 0 0.1657835
cnvi0111198 NC 0 0.9496717 1.25545 0.9779768 -0.04701744
cnvi0111199 NC 0 0.02349442 1.322649 0.00630372 0.05687102
cnvi0111200 NC 0 0.9757202 0.7494568 0.9911757 -0.2348882
cnvi0111201 NC 0 0.03217006 0.9018167 0.01433515 -0.03648386
cnvi0111202 NC 0 0.8904491 1.416932 0.9610257 0.08787975
cnvi0111203 NC 0 0.02859106 1.726395 0.00382948 0.05932779
cnvi0111204 NC 0 0.9785868 1.347865 0.9897895 0.1457004

Total number of rows: 299140

Table truncated, full table size 18147 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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