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Sample GSM182192 Query DataSets for GSM182192
Status Public on May 12, 2008
Title CHD Patient 1812
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 (Ventricular septal defect). 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 -0.147 2367 295 1927 137 0
1_1_2_empty null 421 293 239 136 -75
1_1_3_empty null 1333 287 1090 135 -75
1_1_4_bA208O6 0.041 4745 283 4633 133 0
1_1_5_empty null 291 286 136 134 -75
1_1_6_empty null 295 284 147 132 -75
1_1_7_N0185M11 0.028 4368 291 4227 133 0
1_1_8_N0723M08 -0.066 4428 296 4010 135 0
1_1_9_N0746C04 -0.088 6727 291 6098 132 0
1_1_10_Empty null 1464 287 1283 134 -75
1_1_11_N0148D21 -0.067 6274 283 5767 132 0
1_1_12_N0081G14 -0.028 7483 291 7064 132 0
1_1_13_F0609E06 0.083 8107 292 8259 134 0
1_1_14_N0266L23 0.109 3779 287 3859 133 0
1_1_15_N0736B01 -0.088 4607 284 4116 130 0
1_1_16_N0753J19 0.009 7623 278 7383 130 0
1_1_17_N0472L10 -0.04 5773 278 5375 131 0
1_1_18_N0490A23 0.024 6875 281 6724 131 0
1_1_19_empty null 293 275 145 129 -75
1_1_20_N0007P15 0.028 4828 277 4673 131 0

Total number of rows: 44640

Table truncated, full table size 1876 Kbytes.




Supplementary file Size Download File type/resource
GSM182192.gpr.gz 3.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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