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Sample GSM755639 Query DataSets for GSM755639
Status Public on Jul 01, 2014
Title ccRCC tumor 2.04
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 0.9649674 1.484493 0.9896107 0.03055618
cnvi0111186 NC 0 0.04666144 0.5537249 0.01751582 0.1530047
cnvi0111187 NC 0 0.9597567 1.682871 0.9735662 0.1393086
cnvi0111188 NC 0 0.02026526 1.340373 0.005746732 0.03856991
cnvi0111189 NC 0 0.03526232 1.39974 0.009393055 -0.04315213
cnvi0111190 NC 0 0.03866659 0.4453564 0.001912612 0.3118305
cnvi0111191 NC 0 0.04120419 1.424648 0.01324713 0.3737747
cnvi0111192 NC 0 0.03424 0.9187826 0.007957185 -0.2778637
cnvi0111193 NC 0 0.009708912 1.155974 0 -0.0707145
cnvi0111194 NC 0 0.9770114 1.282348 0.9938532 -0.05340673
cnvi0111195 NC 0 0.04495366 2.100333 0.01314521 0.1052263
cnvi0111196 NC 0 0.9747387 1.024957 0.9910207 -0.2601474
cnvi0111197 NC 0 0.007613912 0.8701922 0 -0.0367991
cnvi0111198 NC 0 0.9569586 1.313605 0.9856775 0.01830937
cnvi0111199 NC 0 0.03301782 1.239489 0.01624484 -0.03681401
cnvi0111200 NC 0 0.9863003 0.7499384 1 -0.2339613
cnvi0111201 NC 0 0.03984579 1.007793 0.02235569 0.1238099
cnvi0111202 NC 0 0.9140151 1.196584 0.9871382 -0.1559691
cnvi0111203 NC 0 0.02650356 1.855682 0.001633664 0.1635153
cnvi0111204 NC 0 0.9853179 1.350701 0.996774 0.1487326

Total number of rows: 299140

Table truncated, full table size 18286 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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