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Sample GSM188133 Query DataSets for GSM188133
Status Public on May 12, 2008
Title CHD Patient 2033
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 (DORV, HLHS) 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 the 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 wereconsidered as genomic aberrations, unless they coincided with a known polymorphism as listed in the Database of Genomic Variants (version Dec 2005)
 
Submission date May 09, 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 -0.141 5886 325 6000 145 0
1_1_2_empty null 488 321 303 145 -75
1_1_3_empty null 1482 314 1383 143 -75
1_1_4_bA208O6 -0.01 5583 315 6236 142 0
1_1_5_empty null 324 309 152 142 -75
1_1_6_empty null 321 311 153 143 -75
1_1_7_N0185M11 -0.068 5037 315 5402 143 0
1_1_8_N0723M08 -0.207 4671 313 4530 143 0
1_1_9_N0746C04 -0.104 6751 312 7066 142 0
1_1_10_Empty null 1503 310 1447 143 -75
1_1_11_N0148D21 -0.065 6706 306 7213 144 0
1_1_12_N0081G14 -0.086 9494 303 10000 145 0
1_1_13_F0609E06 -0.063 9949 302 10630 145 0
1_1_14_N0266L23 0.06 4480 301 5233 143 0
1_1_15_N0736B01 -0.195 4079 312 3974 150 0
1_1_16_N0753J19 0.002 9076 308 10166 149 0
1_1_17_N0472L10 -0.004 5246 302 5886 145 0
1_1_18_N0490A23 -0.067 6769 300 7271 145 0
1_1_19_empty null 299 289 155 140 -75
1_1_20_N0007P15 -0.015 4193 291 4638 139 0

Total number of rows: 44640

Table truncated, full table size 1871 Kbytes.




Supplementary file Size Download File type/resource
GSM188133.gpr.gz 3.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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