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Sample GSM755607 Query DataSets for GSM755607
Status Public on Jul 01, 2014
Title ccRCC tumor 4.08
Sample type genomic
 
Source name clear cell renal cell carcinoma
Organism Homo sapiens
Characteristics tumor stage: un-metastasized tumor
gender: Female
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 0.9702631 1.453496 0.9951823 0.000112472
cnvi0111186 NC 0 0.09247544 0.4131713 0.06596266 -0.2694246
cnvi0111187 NC 0 0.9849439 1.603185 0.9997887 0.06932422
cnvi0111188 NC 0 0.01660142 1.341586 0.001932707 0.03987456
cnvi0111189 NC 0 0.03469282 1.573089 0.00879314 0.1252892
cnvi0111190 NC 0 0.03040166 0.3562383 0 -0.01028701
cnvi0111191 NC 0 0.03900781 1.002915 0.01092796 -0.1326321
cnvi0111192 NC 0 0.02627386 1.069626 0 -0.05855248
cnvi0111193 NC 0 0.02494322 1.167028 0.01159025 -0.05698508
cnvi0111194 NC 0 0.9771257 1.218729 0.9939725 -0.1268169
cnvi0111195 NC 0 0.03805844 2.41217 0.005835225 0.3049399
cnvi0111196 NC 0 0.9689406 1.204664 0.9849732 -0.02707971
cnvi0111197 NC 0 0.005770147 0.9517322 0 0.0924223
cnvi0111198 NC 0 0.9632568 1.013171 0.9923335 -0.3563445
cnvi0111199 NC 0 0.006939931 1.595489 0 0.3274394
cnvi0111200 NC 0 0.9732902 0.8629434 0.9886433 -0.0314674
cnvi0111201 NC 0 0.06532481 0.8432004 0.04897924 -0.1334424
cnvi0111202 NC 0 0.9271793 1.269593 1 -0.07052504
cnvi0111203 NC 0 0.01251903 1.930532 0 0.2205637
cnvi0111204 NC 0 0.9793069 1.043408 0.9905367 -0.2236723

Total number of rows: 299140

Table truncated, full table size 18053 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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