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Sample GSM188149 Query DataSets for GSM188149
Status Public on May 12, 2008
Title CHD Patient 2595
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 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 -0.114 3739 317 3282 139 0
1_1_2_empty null 396 311 215 140 -75
1_1_3_empty null 626 305 459 137 -75
1_1_4_bA208O6 -0.018 3807 303 3577 135 0
1_1_5_empty null 330 298 161 133 -75
1_1_6_empty null 336 296 162 135 -75
1_1_7_N0185M11 -0.034 4320 297 4040 133 0
1_1_8_N0723M08 0.004 3962 293 3790 129 0
1_1_9_N0746C04 -0.043 7529 293 7245 130 0
1_1_10_Empty null 1083 299 1001 136 -75
1_1_11_N0148D21 0.003 6731 322 6659 163 0
1_1_12_N0081G14 -0.05 6973 318 6655 154 0
1_1_13_F0609E06 -0.07 7891 310 7470 147 0
1_1_14_N0266L23 0.011 3154 295 3003 133 0
1_1_15_N0736B01 -0.089 4265 288 3831 125 0
1_1_16_N0753J19 -0.068 5802 287 5392 124 0
1_1_17_N0472L10 0.027 8513 271 8680 120 0
1_1_18_N0490A23 -0.24 6643 271 5520 118 0
1_1_19_empty null 301 276 148 119 -75
1_1_20_N0007P15 -0.02 4901 278 4663 117 0

Total number of rows: 44640

Table truncated, full table size 1872 Kbytes.




Supplementary file Size Download File type/resource
GSM188149.gpr.gz 3.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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