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Sample GSM816587 Query DataSets for GSM816587
Status Public on Feb 06, 2013
Title BLD2_P-38
Sample type genomic
 
Source name peripheral blood
Organism Homo sapiens
Characteristics sample type: peripheral blood
cell_type: lymphocyte
patient: P-38
gender: female
age: 47
transplanted organ: kidney
immunosuppressive drugs: azathioprine + prednison
Extracted molecule genomic DNA
Extraction protocol DNA was isolated from SCC and AK samples that contained at least 70% tumor cells, as determined by haematoxylin and eosin stained frozen sections. DNA from the tumor samples was isolated using the Genomic-tips 20/G kit (Qiagen). A salting-out procedure was used to isolate genomic DNA from the peripheral blood samples. DNA was quantified using a Nanodrop (NanoDrop technologies) and evaluated for degradation on agarose gel.
Label C-Bio and A-DNP
Label protocol 400 ng of genomic DNA was labelled according to Illumina's standard protocol
 
Hybridization protocol Hybridizations were performed at the Leiden Genome Technology Center according to the manufacturer's instructions
Scan protocol The beadChips were scanned using the Illumina BeadArray Reader, using the standard Illumina scanning protocol
Data processing Image analysis and quality control (call rate > 98%) was performed in Illumina's BeadStudio Version 3.2 software using the genotyping module. Each BeadChip was self-normalized using information contained within the array. Further analysis and visualization was performed with the Illumina Genome Viewer in Beadstudio. First, tumor data was paired with data from their corresponding normal control. Subsequently, examination of the log R ratio (signal intensity tumor/signal intensity normal control) and B allele frequency (BAF) was analyzed for the presence of copy number variations (CNVs) and/or loss of heterozygosity (LOH) in the tumor samples. By plotting the log R ratio across a chromosome, CNVs could be visualized by an increase or decrease in baseline signal. Secondly, the BAF was plotted across each chromosome to detect regions of LOH in tumor cells. A region with LOH was defined as a stretch of heterozygous SNPs in normal DNA but homozygous in the matched tumor DNA.
Matrix signal (ie, The signal intensities of all SNPs for each sample) is linked as a supplementary file on the Series record.
 
Submission date Oct 13, 2011
Last update date Feb 06, 2013
Contact name Harry Vrieling
E-mail(s) h.vrieling@lumc.nl
Organization name Leiden University Medical Center
Department Toxicogenetics, S4-P
Lab room T4-34
Street address Einthovenweg 20
City Leiden
ZIP/Postal code 2333 ZC
Country Netherlands
 
Platform ID GPL6982
Series (2)
GSE32969 Genome-wide SNP analysis of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients
GSE32979 Cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients

Data table header descriptions
ID_REF
VALUE Gtype (Genotype)
BLD2_P.38.Score
BLD2_P.38.Theta
BLD2_P.38.R
BLD2_P.38.B.Allele.Freq
BLD2_P.38.Log.R.Ratio

Data table
ID_REF VALUE BLD2_P.38.Score BLD2_P.38.Theta BLD2_P.38.R BLD2_P.38.B.Allele.Freq BLD2_P.38.Log.R.Ratio
MitoA10045G-13273284_B_R_IFB1141652022:0 AA 0.3066981 0.003191405 2.870664 0 -0.6694671
MitoA10551G-13273286_T_F_IFB1141639111:0 AA 0.298474 0.01806737 3.781614 0 -0.5663698
MitoA11252G-13273288_B_R_IFB1141661584:0 BB 0.329167 0.9815284 2.222517 1 -0.1044718
MitoA11468G-13273289_B_R_IFB1141719645:0 AA 0.3187215 0.01273007 4.035548 0 -0.646565
MitoA11813G-13273292_T_F_IFB1141667833:0 AA 0.2514375 0.04715922 3.406585 0.003424114 -0.6098919
MitoA12309G-13273294_T_F_IFB1141664161:0 AA 0.283866 0.01817615 3.017686 0 -0.7140199
MitoA13106G-13273298_B_R_IFB1141641623:0 AA 0.3484128 0.02502183 1.429172 0.002866535 -0.1334817
MitoA13264G-13273299_T_F_IFB1141660858:0 AA 0.2567114 0.02193292 4.50736 0 -0.5787844
MitoA13781G-13273301_T_F_IFB1141687043:0 AA 0.3312233 0.05706474 0.5070359 0.009823075 -1.329367
MitoA14234G-13273304_T_F_IFB1141674277:0 AA 0.3183387 0.0138647 1.7037 0 -0.9579588
MitoA14583G-13273306_T_F_IFB1141688843:0 AA 0.329661 0.008135806 1.395499 0 -0.7002164
MitoA15219G-13273311_T_F_IFB1141717824:0 AA 0.2632663 0.06590933 2.717786 0.01047052 -0.9254142
MitoA15245G-13273312_B_R_IFB1141677374:0 AA 0.319456 0.03083231 2.189875 0 -0.3018068
MitoA15302G-13273313_T_F_IFB1141686491:0 BB 0.2665412 0.9370077 2.2411 1 -0.1497141
MitoA15759G-13273316_B_R_IFB1141715135:0 AA 0.3469829 0.01125278 4.335312 0 -0.5503414
MitoA15925G-13273318_T_F_IFB1141694300:0 AA 0.2904017 0.02681977 3.0851 0 -0.3528877
MitoA16163G-13273319_T_F_IFB1141711520:0 AA 0.2527641 0.06967785 4.123837 0.02735283 -0.6363326
MitoA16164G-13273320_T_F_IFB1141715312:0 AA 0.3119528 0.01671428 2.475039 0 -0.8603808
MitoA1738G-13273322_T_F_IFB1141639534:0 AA 0.3015448 0.01432327 4.411497 0 -0.4730331
MitoA3349G-13273328_T_F_IFB1141711832:0 AA 0.2904017 0.04225626 5.189717 0.01293805 -0.4407318

Total number of rows: 561466

Table truncated, full table size 46502 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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