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Sample GSM755606 Query DataSets for GSM755606
Status Public on Jul 01, 2014
Title kidney cortex 4.08
Sample type genomic
 
Source name kidney cortex
Organism Homo sapiens
Characteristics tumor stage: not applicable
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 normal kidney cortex 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 0.964371 1.410686 0.9889833 -0.04301729
cnvi0111186 NC 0 0.03417232 0.6807151 0.004308964 0.4508867
cnvi0111187 NC 0 0.975872 1.444207 0.9903439 -0.08133854
cnvi0111188 NC 0 0.01772178 1.264991 0.003098996 -0.0449376
cnvi0111189 NC 0 0.03014619 1.356319 0.004003752 -0.08861478
cnvi0111190 NC 0 0.009791159 0.4619614 0 0.3646424
cnvi0111191 NC 0 0.0409842 0.9863359 0.01301484 -0.1566802
cnvi0111192 NC 0 0.03446687 1.025786 0.008196245 -0.1189292
cnvi0111193 NC 0 0.03260106 1.208994 0.01955434 -0.006017133
cnvi0111194 NC 0 0.9708598 1.306089 0.9874341 -0.0269411
cnvi0111195 NC 0 0.04553832 1.845857 0.01376505 -0.08110065
cnvi0111196 NC 0 0.9662885 1.105511 0.9822071 -0.1509974
cnvi0111197 NC 0 0.02215506 1.026628 0.00982191 0.2017089
cnvi0111198 NC 0 0.9568747 1.252177 0.9855888 -0.05078366
cnvi0111199 NC 0 0.03407326 1.298065 0.01734657 0.02980333
cnvi0111200 NC 0 0.9824847 0.877507 0.9982251 -0.007322656
cnvi0111201 NC 0 0.03777061 0.9251419 0.02018728 0.000356648
cnvi0111202 NC 0 0.9010224 1.354038 0.9727415 0.0223778
cnvi0111203 NC 0 0.03516494 1.587384 0.01074445 -0.06178324
cnvi0111204 NC 0 0.9835106 1.232949 0.9948987 0.01713786

Total number of rows: 299140

Table truncated, full table size 18170 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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