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Sample GSM1553898 Query DataSets for GSM1553898
Status Public on Jul 30, 2015
Title 960M
Sample type genomic
 
Channel 1
Source name lymph node metastasis
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 0.0913
CHR01FS000052308 0.2197
CHR01FS000357503 0.0319
CHR01FS000443361 0.1203
CHR01FS000530358 0.1268
CHR01FS000547649 -0.0002
CHR01FS000560348 0.3392
CHR01FS000580411 0.2949
CHR01FS000614850 0.3945
CHR01FS000722938 -0.1045
CHR01FS000750232 0.0201
CHR01FS000782679 -0.0507
CHR01FS001018317 -0.0678
CHR01FS001069258 -0.3238
CHR01FS001099612 -0.3763
CHR01FS001314689 -0.0146
CHR01FS001315417 0.3846
CHR01FS001400200 -0.1876
CHR01FS001457534 0.1475
CHR01FS001489998 -0.0930

Total number of rows: 134937

Table truncated, full table size 3223 Kbytes.




Supplementary file Size Download File type/resource
GSM1553898_960M_532.pair.gz 2.5 Mb (ftp)(http) PAIR
GSM1553898_960M_635.pair.gz 2.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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