NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1553943 Query DataSets for GSM1553943
Status Public on Jul 30, 2015
Title 911T
Sample type genomic
 
Channel 1
Source name primary tumor
Organism Homo sapiens
Characteristics gender: female
Extracted molecule genomic DNA
Extraction protocol DNA from solid tissues was isolated using standard phenol – chloroform extraction method (Sambrook, J., Russell, D.W., 2001, Molecular Cloning: A Laboratory Manual, Volume 1st of 3, 6.4-6.12, Cold Spring Harbor Laboratory Press, ISBN 9780879695774) with modifications. DNA from blood samples was isolated by QIAamp DNA Blood Kit according to manufacturer’s protocol (QIAamp DNA Blood Midi Kit, QIAGEN, Hilden, Germany, #5118).
Label Cy3
Label protocol Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).
 
Channel 2
Source name uninvolved glandular tissue
Organism Homo sapiens
Characteristics gender: female
Extracted molecule genomic DNA
Extraction protocol DNA from solid tissues was isolated using standard phenol – chloroform extraction method (Sambrook, J., Russell, D.W., 2001, Molecular Cloning: A Laboratory Manual, Volume 1st of 3, 6.4-6.12, Cold Spring Harbor Laboratory Press, ISBN 9780879695774) with modifications. DNA from blood samples was isolated by QIAamp DNA Blood Kit according to manufacturer’s protocol (QIAamp DNA Blood Midi Kit, QIAGEN, Hilden, Germany, #5118).
Label Cy5
Label protocol Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).
 
 
Hybridization protocol Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).
Scan protocol Sample labeling, hybridization, washing and two-color scanning was performed according to Nimblegen’s protocol with modification as previously described (Ronowicz et al. 2012, Anal Biochem. 426:91-3, PMID: 22504026).
Description Comparative Genomic Hybridization of tissues from breast cancer patients
Data processing Microarray data were extracted with DEVA software v1.2 CGH, including spatial correction (LOESS) and qspline fit normalization, in order to compensate for differences in signal between the two dyes (Workman et al., 2002, Genome Biol 3(9):research0048, PMID: 12225587).
 
Submission date Nov 25, 2014
Last update date Jul 30, 2015
Contact name Arkadiusz Piotrowski
Organization name Medical University of Gdansk
Department Biology and Pharmaceutical Botany
Lab Microarray Facility
Street address Hallera 107
City Gdansk
ZIP/Postal code 80-416
Country Poland
 
Platform ID GPL16707
Series (1)
GSE63623 Concurrent DNA copy number alterations and mutations in genes related to maintenance of genome stability in uninvolved glandular tissue from breast cancer patients

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3 vs Cy5)

Data table
ID_REF VALUE
CHR01FS000037196 0.2188
CHR01FS000052308 0.4243
CHR01FS000357503 0.1129
CHR01FS000443361 0.1121
CHR01FS000530358 0.0041
CHR01FS000547649 0.1572
CHR01FS000560348 0.4949
CHR01FS000580411 0.5654
CHR01FS000614850 0.4363
CHR01FS000722938 -0.0894
CHR01FS000750232 -0.3193
CHR01FS000782679 -0.3878
CHR01FS001018317 -0.3520
CHR01FS001069258 -0.6066
CHR01FS001099612 -0.6318
CHR01FS001314689 -0.1995
CHR01FS001315417 0.0202
CHR01FS001400200 -0.5450
CHR01FS001457534 -0.1989
CHR01FS001489998 -0.4063

Total number of rows: 134937

Table truncated, full table size 3221 Kbytes.




Supplementary file Size Download File type/resource
GSM1553943_911T_532.pair.gz 2.5 Mb (ftp)(http) PAIR
GSM1553943_911T_635.pair.gz 2.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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