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Sample GSM755694 Query DataSets for GSM755694
Status Public on Jul 01, 2014
Title ccRCC tumor 7.06
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 0.9655616 1.60077 0.9902359 0.1393523
cnvi0111186 NC 0 0.03959942 0.5830373 0.01004795 0.2274235
cnvi0111187 NC 0 0.9757171 1.461964 0.9901826 -0.06370848
cnvi0111188 NC 0 0.03250572 1.27083 0.01848894 -0.03829332
cnvi0111189 NC 0 0.02732106 1.413824 0.001027786 -0.02870818
cnvi0111190 NC 0 0.02865971 0.5473915 0 0.6094432
cnvi0111191 NC 0 0.04431944 0.8396137 0.01653652 -0.3890336
cnvi0111192 NC 0 0.03463918 0.9766389 0.008377823 -0.189762
cnvi0111193 NC 0 0.02360258 1.153435 0.01019599 -0.07388727
cnvi0111194 NC 0 0.9725121 1.077371 0.9891583 -0.3046791
cnvi0111195 NC 0 0.03960847 1.998636 0.007478487 0.03362397
cnvi0111196 NC 0 0.9828658 1.037728 0.9994973 -0.2422824
cnvi0111197 NC 0 0.02536058 1.006927 0.01315192 0.1737546
cnvi0111198 NC 0 0.9701726 1.281685 0.9996421 -0.0171802
cnvi0111199 NC 0 0.0244583 1.191393 0.00730988 -0.09391019
cnvi0111200 NC 0 0.9726459 0.8835968 0.9879719 0.00265486
cnvi0111201 NC 0 0.03693545 0.9086114 0.01931461 -0.02565456
cnvi0111202 NC 0 0.8921406 1.367388 0.9628999 0.03653166
cnvi0111203 NC 0 0.03932946 1.663521 0.01512505 0.005805788
cnvi0111204 NC 0 0.9840248 1.20389 0.9954323 -0.01727175

Total number of rows: 299140

Table truncated, full table size 18280 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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