NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM951496 Query DataSets for GSM951496
Status Public on Jan 01, 2014
Title 44 Tumor
Sample type genomic
 
Channel 1
Source name Patient 44 Tumor DNA
Organism Homo sapiens
Characteristics patient: 44
tissue: Tumor
molecular subtype: luminal
gender: Female
er_ihc_score: 90
pr_ihc_score: 75
age: 41
previoustreatment: HighDensityTreatment
numberpositivelymphnodes: 10LN
tumorstage: 2
grade: Grade II
recurrencefreesurvival: 4632
overalstatus: alive
overallsurvival: 4632
p53_ihc: 0
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from 10 10 m-thick paraffin-embedded tissue sections. Sections were deparaffinated twice for 5 min in xylene, rehydrated in 100, 96 and 70% ethanol for 30 s each, stained with haematoxylin for 30 s, rinsed with water and incubated overnight in 1 m NaSCN at 37°C to remove crosslinks. Slides were rinsed twice 10 min in 1 PBS at room temperature, and completely air-dried. Tumour tissue was scraped from the glass with a scalpel to obtain at least 70% tumour cells in 200 l Qiagen ATL buffer (QIAamp® DNA extraction kit cat. 51306), transferred to eppendorf tubes and incubated with 27 l proteinase-K (20 mg/ml stock) at 450 rpm (Eppendorf® Thermomixer R) at 55°C. Three more aliquots of 27 l proteinase-K were added at 4, 20 and 28 h. After a total protK incubation of 44 h, DNA isolation proceeded as in the manufacturer's protocol (Qiagen, Cat. 51306). Samples of isolated genomic DNA were analysed by 0.8% agarose gel electrophoresis to visualise DNA concentration and size distribution. In case of tumour tissue, we scraped regions containing at least 70% tumour as indicated by an experienced breast cancer pathologist.
Label Cy3
Label protocol Labeling was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer's instructions (Enzo Life Sciences). Briefly, 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 μl. The DNA was denatured at 99°C for 10 min, and placed on ice. While on ice, 10 μl cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 μl Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37°C, 5 μl stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit (Qiagen, Westburg, Leusden, NL).
 
Channel 2
Source name Megapool reference DNA female, EA-100F
Organism Homo sapiens
Characteristics gender: Female
sample type: control
Extracted molecule genomic DNA
Extraction protocol aCGH reference DNA was isolated from peripheral blood lymphocytes from six apparently healthy female individuals. It was pooled and sonicated until its median fragment length was similar to that of the test samples.
Label Cy5
Label protocol Labeling was performed using the Enzo Genomic DNA Labeling kit according to the manufacturer's instructions (Enzo Life Sciences). Briefly, 500 ng genomic DNA was combined with a mixture of primers and reaction buffer to a final volume of 39 μl. The DNA was denatured at 99°C for 10 min, and placed on ice. While on ice, 10 μl cyanine 3-dUTP and cyanine 5-dUTP nucleotide mixture was added to the test and reference DNA, respectively, and finally 1 μl Klenow DNA polymerase was added to each sample to extend the primers. After 4 hr incubation at 37°C, 5 μl stop buffer was added to stop the reaction. Label was purified using the QIAquick PCR Purification Kit (Qiagen, Westburg, Leusden, NL).
 
 
Hybridization protocol Labelled DNA was hybridized on a 720K Nimblegen CGH array (human CGH 3x720k whole-genome tiling v3.1 arrays: GPL14965 and GPL15436), containing 719690 unique in situ synthesized 60-mer oligonucleotides, according to manufacturer’s protocol (Roche Nimblegen, Madison, USA).
Scan protocol Slides of the arrays were scanned using a G2505C microarray scanner (Agilent Technologies).
Description 444697A01
Data processing Data was processed using the NimbleScan sorftware provided by the vendor. The RATIO_CORRECTED value, a background corrected log2 ratio of the two color channels, was used in all subsequent analyses.
 
Submission date Jun 22, 2012
Last update date Jan 01, 2014
Contact name Christiaan Nicolaas Klijn
E-mail(s) c.klijn@gmail.com
Phone +31-205122004
Organization name Genentech
Department Bioinformatics and Computational Biology
Lab Genomics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country Netherlands
 
Platform ID GPL15436
Series (1)
GSE38888 Lack of genetic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases

Data table header descriptions
ID_REF
VALUE background corrected log2(tumor/normal)

Data table
ID_REF VALUE
CHR10FS057882816 0.346
CHR10FS104954995 -0.514
CHR10FS073146205 -0.245
CHR10FS074415436 0.13
CHR10FS056433745 0.339
CHR10FS042465705 0.203
CHR10FS034915368 0.196
CHR10FS111129462 -0.304
CHR10FS030218255 0.045
CHR10FS064927986 0.003
CHR10FS076646158 0.041
CHR10FS008849582 0.264
CHR10FS013270397 -0.22
CHR10FS073935878 0.335
CHR10FS003132996 0.029
CHR10FS100519470 -0.5
CHR10FS024506966 0.08
CHR10FS103792296 -0.223
CHR10FS063334259 0.152
CHR10FS085180149 0.201

Total number of rows: 719690

Table truncated, full table size 16381 Kbytes.




Supplementary file Size Download File type/resource
GSM951496_444697A01_MAF_S01_crop_532.pair.gz 12.3 Mb (ftp)(http) PAIR
GSM951496_444697A01_MAF_S01_crop_635.pair.gz 12.4 Mb (ftp)(http) PAIR
Processed data included within Sample table

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