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Sample GSM1553978 Query DataSets for GSM1553978
Status Public on Jul 30, 2015
Title 914M
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 0.4402
CHR01FS000052308 0.9204
CHR01FS000357503 0.4528
CHR01FS000443361 0.4768
CHR01FS000530358 0.4348
CHR01FS000547649 0.4398
CHR01FS000560348 0.9248
CHR01FS000580411 1.0054
CHR01FS000614850 1.0013
CHR01FS000722938 0.5679
CHR01FS000750232 -0.1890
CHR01FS000782679 -0.2015
CHR01FS001018317 -0.1240
CHR01FS001069258 -0.2200
CHR01FS001099612 -0.4332
CHR01FS001314689 -0.1332
CHR01FS001315417 0.3193
CHR01FS001400200 -0.3014
CHR01FS001457534 0.1582
CHR01FS001489998 0.0806

Total number of rows: 134937

Table truncated, full table size 3219 Kbytes.




Supplementary file Size Download File type/resource
GSM1553978_914M_532.pair.gz 2.5 Mb (ftp)(http) PAIR
GSM1553978_914M_635.pair.gz 2.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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