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Sample GSM182170 Query DataSets for GSM182170
Status Public on May 12, 2008
Title CHD Patient 1616
Sample type genomic
 
Channel 1
Source name DNA isolated from blood
Organism Homo sapiens
Characteristics DNA isolated from blood of a patient with congenital heart disease (Transposition of the great arteria). Gender: male
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from peripheral blood by a salting out procedure (Grimberg et al.,1989).
Label Cy3
Label protocol Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
 
Channel 2
Source name DNA isolated from blood
Organism Homo sapiens
Characteristics DNA isolated from blood of a healthy male donor
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from peripheral blood by a salting out procedure (Blin and Stafford,1976).
Label Cy5
Label protocol Probes were labelled by random priming. Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
 
 
Hybridization protocol Hybridization was done overnight at 42°C in a slide booster (Advalytix, Brunnthal, Germany). Detailed protocols are available at our website (Molecular Cytogenetics at the Max Planck Institute for Molecular Genetics)
Scan protocol Slides were scanned using an Agilent scanner .
Description Array CGH analysis of a patient with congenital heart disease
Data processing TIFF images were analysed by Genepix 5.0 (Axon Instruments, Union City, CA) and raw intensities (gpr files) were imported into CGHPRO (Chen at al.,2005). Background intensities were not substracted. Signal intensities were normalized by subgridd LOWESS. Aberrant ratios involving three or more neighbouring clones were considered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants (version Dec 2005)
 
Submission date Apr 16, 2007
Last update date May 12, 2008
Contact name Fikret Erdogan
E-mail(s) erdogan@molgen.mpg.de
Organization name Max-Planck-Institute
Street address Ihnestr. 73
City Berlin
ZIP/Postal code 14195
Country Germany
 
Platform ID GPL5000
Series (1)
GSE7527 Array CGH in congenital heart disease

Data table header descriptions
ID_REF
VALUE normalized log ratio (subgrid lowess)
f635Mean foreground signal intensity Cy5
b635Mean background signal intensity Cy5
f532Mean foreground signal intensity Cy3
b532Mean background signal intensity Cy3
Flags 0: valid spots -50: clones with unverified chromosomal positions -75: empty Spots -100: excluded

Data table
ID_REF VALUE f635Mean b635Mean f532Mean b532Mean Flags
1_1_1_bK2185H17 -0.123 3050 270 2584 96 0
1_1_2_empty null 559 270 350 93 -75
1_1_3_empty null 361 273 197 95 -75
1_1_4_bA208O6 -0.03 2215 275 1942 97 0
1_1_5_empty null 263 265 95 88 -75
1_1_6_empty null 261 265 93 86 -75
1_1_7_N0185M11 -0.07 1513 263 1261 88 0
1_1_8_N0723M08 0.013 1749 264 1567 91 0
1_1_9_N0746C04 -0.051 2306 268 1996 94 0
1_1_10_Empty null 368 257 210 89 -75
1_1_11_N0148D21 -0.063 3174 259 2812 89 0
1_1_12_N0081G14 -0.005 2601 263 2358 89 0
1_1_13_F0609E06 0.034 3203 270 3037 100 0
1_1_14_N0266L23 0.043 1345 265 1203 98 0
1_1_15_N0736B01 -0.016 1745 252 1532 85 0
1_1_16_N0753J19 0.027 2667 258 2481 85 0
1_1_17_N0472L10 0.002 2807 264 2579 88 0
1_1_18_N0490A23 0.026 3318 260 3131 87 0
1_1_19_empty null 272 263 97 88 -75
1_1_20_N0007P15 0.069 1859 269 1737 89 0

Total number of rows: 44640

Table truncated, full table size 1823 Kbytes.




Supplementary file Size Download File type/resource
GSM182170.gpr.gz 2.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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