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Sample GSM1553997 Query DataSets for GSM1553997
Status Public on Jul 30, 2015
Title 903H
Sample type genomic
 
Channel 1
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 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 peripheral blood leukocytes
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 GPL15436
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
CHR01FS000032108 -0.3193
CHR01FS000036566 0.0275
CHR01FS000037196 -0.7109
CHR01FS000038109 -0.3832
CHR01FS000039532 -0.3598
CHR01FS000049283 -0.2583
CHR01FS000052308 -0.7333
CHR01FS000055650 -1.2023
CHR01FS000059489 -0.3012
CHR01FS000060884 -0.5443
CHR01FS000072260 0.0360
CHR01FS000241735 -0.4407
CHR01FS000357503 -0.0737
CHR01FS000389471 -0.2052
CHR01FS000403676 -0.1796
CHR01FS000443361 -0.7402
CHR01FS000530358 -0.1817
CHR01FS000532718 -0.3616
CHR01FS000547649 -0.3288
CHR01FS000553694 0.1967

Total number of rows: 719690

Table truncated, full table size 17180 Kbytes.




Supplementary file Size Download File type/resource
GSM1553997_903H_532.pair.gz 13.6 Mb (ftp)(http) PAIR
GSM1553997_903H_635.pair.gz 13.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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