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Sample GSM1554033 Query DataSets for GSM1554033
Status Public on Jul 30, 2015
Title 915M
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 GPL19457
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
CHR01FS000010481 -0.0364
CHR01FS000010551 0.0228
CHR01FS000010593 0.2150
CHR01FS000010807 0.3763
CHR01FS000010873 0.3232
CHR01FS000010991 0.0680
CHR01FS000011043 0.2750
CHR01FS000011097 0.4300
CHR01FS000011247 0.0975
CHR01FS000011351 -0.1109
CHR01FS000011419 0.0586
CHR01FS000012747 -0.2414
CHR01FS000012821 -0.4009
CHR01FS000013073 -0.2738
CHR01FS000013233 -0.2412
CHR01FS000013291 -0.1736
CHR01FS000013943 0.0472
CHR01FS000014225 0.0461
CHR01FS000014569 -0.4745
CHR01FS000014701 -0.6080

Total number of rows: 720147

Table truncated, full table size 17148 Kbytes.




Supplementary file Size Download File type/resource
GSM1554033_915M_532.pair.gz 12.1 Mb (ftp)(http) PAIR
GSM1554033_915M_635.pair.gz 12.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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