NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM755703 Query DataSets for GSM755703
Status Public on Jul 01, 2014
Title ccRCC tumor 7.34-3D
Sample type genomic
 
Source name clear cell renal cell carcinoma
Organism Homo sapiens
Characteristics tumor stage: un-metastasized tumor
gender: Male
tissue: Kidney
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 clear cell renal cell carcinoma tumors 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 0.9701024 1.032492 0.9950134 -0.4932837
cnvi0111186 NC 0 0.0539351 0.4079382 0.02520747 -0.2878141
cnvi0111187 NC 0 0.9755355 1.13112 0.9899935 -0.4338647
cnvi0111188 NC 0 0.02366895 1.080458 0.009289945 -0.2724214
cnvi0111189 NC 0 0.03643441 1.312029 0.01062772 -0.1365116
cnvi0111190 NC 0 0.02666079 0.7387307 0 1.041919
cnvi0111191 NC 0 0.02829186 1.294098 0 0.2351153
cnvi0111192 NC 0 0.01081323 1.004272 0 -0.1495096
cnvi0111193 NC 0 0.07084079 0.5143225 0.05932333 -1.239079
cnvi0111194 NC 0 0.9891131 1.233812 1 -0.1090723
cnvi0111195 NC 0 0.03817301 2.275756 0.005956681 0.2209545
cnvi0111196 NC 0 0.9907393 1.051775 1 -0.2228842
cnvi0111197 NC 0 0.01295247 1.193505 0.000261949 0.4189995
cnvi0111198 NC 0 0.9727387 0.9741481 1 -0.4130088
cnvi0111199 NC 0 0.01766877 1.396435 0.00022254 0.1351893
cnvi0111200 NC 0 0.981387 1.031038 0.997081 0.2252925
cnvi0111201 NC 0 0.02353475 0.6432288 0.00531193 -0.5239861
cnvi0111202 NC 0 0.9418065 1.414571 1 0.08547375
cnvi0111203 NC 0 0.01103778 1.861659 0 0.1681546
cnvi0111204 NC 0 0.9800462 1.060165 0.9913038 -0.2006866

Total number of rows: 299140

Table truncated, full table size 17977 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap