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Sample GSM755608 Query DataSets for GSM755608
Status Public on Jul 01, 2014
Title peripheral blood 4.10
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 0.9601842 1.445941 0.9845782 -0.007405024
cnvi0111186 NC 0 0.0256422 0.7317822 0 0.5552498
cnvi0111187 NC 0 0.9770676 1.730161 0.9915887 0.1792898
cnvi0111188 NC 0 0.02419484 1.43873 0.009837391 0.1407312
cnvi0111189 NC 0 0.02862114 1.363 0.002397273 -0.08152551
cnvi0111190 NC 0 0.02362601 0.5397884 0 0.5892643
cnvi0111191 NC 0 0.04898446 1.153298 0.02146232 0.06893372
cnvi0111192 NC 0 0.04131037 1.039616 0.01540768 -0.09960864
cnvi0111193 NC 0 0.02663879 1.289138 0.01335363 0.0865825
cnvi0111194 NC 0 0.9723088 1.296705 0.9889461 -0.03734436
cnvi0111195 NC 0 0.04948719 1.820943 0.01795145 -0.1007056
cnvi0111196 NC 0 0.9689887 1.191189 0.9850234 -0.04330773
cnvi0111197 NC 0 0.01680718 0.9967207 0.004266348 0.159056
cnvi0111198 NC 0 0.9504315 1.346117 0.9787797 0.0535824
cnvi0111199 NC 0 0.03291564 1.056295 0.01613818 -0.2675472
cnvi0111200 NC 0 0.9810633 0.9888914 0.9967438 0.1650787
cnvi0111201 NC 0 0.02422282 1.005373 0.006030911 0.1203417
cnvi0111202 NC 0 0.8699532 1.464809 0.938315 0.1358214
cnvi0111203 NC 0 0.04494902 1.757072 0.02103619 0.08473914
cnvi0111204 NC 0 0.976032 1.252311 0.9871385 0.03961757

Total number of rows: 299140

Table truncated, full table size 18258 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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