NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM182193 Query DataSets for GSM182193
Status Public on May 12, 2008
Title CHD Patient 1815
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 (Atrial Septal Defect). Gender: female
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 female 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 -0.244 4209 294 4759 125 0
1_1_2_empty null 535 293 382 126 -75
1_1_3_empty null 446 297 309 129 -75
1_1_4_bA208O6 -0.056 2856 290 3679 124 0
1_1_5_empty null 329 283 155 122 -75
1_1_6_empty null 349 286 178 123 -75
1_1_7_N0185M11 -0.048 2580 306 3302 135 0
1_1_8_N0723M08 0.005 2881 302 3875 131 0
1_1_9_N0746C04 -0.028 5795 289 7625 121 0
1_1_10_Empty null 887 283 984 119 -75
1_1_11_N0148D21 -0.038 4840 285 6399 120 0
1_1_12_N0081G14 0.036 5085 288 7029 118 0
1_1_13_F0609E06 0.253 5244 290 8383 118 0
1_1_14_N0266L23 0.142 2365 283 3449 119 0
1_1_15_N0736B01 -0.02 3986 287 5269 121 0
1_1_16_N0753J19 0.002 5435 290 7312 120 0
1_1_17_N0472L10 -0.051 3840 291 4959 119 0
1_1_18_N0490A23 0.286 3170 291 5174 119 0
1_1_19_empty null 326 281 180 115 -75
1_1_20_N0007P15 0.03 3339 281 4563 116 0

Total number of rows: 44640

Table truncated, full table size 1841 Kbytes.




Supplementary file Size Download File type/resource
GSM182193.gpr.gz 3.0 Mb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap