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Sample GSM182183 Query DataSets for GSM182183
Status Public on May 12, 2008
Title CHD Patient 1693
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 (Pulmonary stenosis). 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 0.169 4711 259 5962 138 0
1_1_2_empty null 919 261 920 136 -75
1_1_3_empty null 464 260 387 133 -75
1_1_4_bA208O6 -0.048 3398 263 3664 138 0
1_1_5_empty null 262 265 152 138 -75
1_1_6_empty null 265 263 156 136 -75
1_1_7_N0185M11 -0.045 2843 268 3057 144 0
1_1_8_N0723M08 -0.043 3179 269 3436 145 0
1_1_9_N0746C04 -0.011 4197 270 4693 143 0
1_1_10_Empty null 515 259 441 138 -75
1_1_11_N0148D21 0.042 5703 265 6637 144 0
1_1_12_N0081G14 0.04 4075 257 4720 139 0
1_1_13_F0609E06 0.013 6354 253 7253 136 0
1_1_14_N0266L23 -0.025 2973 252 3253 135 0
1_1_15_N0736B01 -0.026 3457 245 3791 131 0
1_1_16_N0753J19 0.047 5541 247 6463 133 0
1_1_17_N0472L10 0.059 5042 245 5918 132 0
1_1_18_N0490A23 0.164 3147 270 3932 157 0
1_1_19_empty null 244 260 146 145 -75
1_1_20_N0007P15 0.086 3118 251 3686 136 0

Total number of rows: 44640

Table truncated, full table size 1857 Kbytes.




Supplementary file Size Download File type/resource
GSM182183.gpr.gz 2.9 Mb (ftp)(http) GPR
Processed data included within Sample table

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