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Sample GSM417861 Query DataSets for GSM417861
Status Public on Jul 10, 2009
Title MR2625 (T20S4-A)
Sample type genomic
 
Channel 1
Source name T20S4-A
Organism Homo sapiens
Characteristics tissue: Ductal Breast Carcinoma
Extracted molecule genomic DNA
Extraction protocol Qiagen Genomic DNA Isolation Kit (cat# 51306).
Label Cy5
Label protocol Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.
 
Channel 2
Source name SKN1
Organism Homo sapiens
Characteristics cell line: EBV Immortalized Fibroblast Reference
Extracted molecule genomic DNA
Extraction protocol Qiagen Genomic DNA Isolation Kit (cat# 51306).
Label Cy3
Label protocol Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.
 
 
Hybridization protocol Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.
Scan protocol Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um.
Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).
Description This sample was hybridized to a single array (two color-reversals not performed).
Data processing The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.
 
Submission date Jun 17, 2009
Last update date Jul 09, 2009
Contact name Nicholas Navin
Organization name Cold Spring Harbor Laboratory
Lab Wigler Lab
Street address 1 Bungtown Road
City Cold Spring Harbor
State/province NY
ZIP/Postal code 11724
Country USA
 
Platform ID GPL8720
Series (2)
GSE16669 Tumor T20 Sectors
GSE16672 All Tumor Sector Experiments (T1-T20)

Data table header descriptions
ID_REF
F635.MEAN Mean of pixel values for each spot scanned at 635 nm wavelength
F532.MEAN Mean of pixel values for each spot scanned at 532 nm wavelength
LOWRED Lowess normalized value for each spot in red colour
LOWGREEN Lowess normalizad value for each spot in green colour
LOCAL.RED Local normalized output for each spot in red
LOCAL.GREEN Local normalized value for each spot in green
LOCAL.RATIO Ratio of local-normalized values for each spot
VALUE log2 of PRE_VALUE
PRE_VALUE Geometric mean Ratio (test/reference) of Two Normalized Channels (Cy5 and Cy3)

Data table
ID_REF F635.MEAN F532.MEAN LOWRED LOWGREEN LOCAL.RED LOCAL.GREEN LOCAL.RATIO VALUE PRE_VALUE
1 641.933 394.711 638.942 392.332 .892502 .555915 1.60546 0.6830 1.60546
2 3347.2 3582.09 3275.52 3585.62 2.96929 3.27884 .905593 -0.1431 .905593
3 248.969 270.524 259.191 263.806 .31023 .302926 1.02411 0.0344 1.02411
4 6993.51 6824.4 6829.98 6793.56 6.38636 6.07739 1.05084 0.0715 1.05084
5 312.156 268.52 319.987 261.73 .323421 .25562 1.26524 0.3394 1.26524
6 118.756 182.796 136.977 172.539 .194122 .238384 .814324 -0.2963 .814324
7 1046.38 566.907 1031.09 568.851 1.54088 .88719 1.73681 0.7964 1.73681
8 1243.01 657.227 1222.33 661.643 1.31823 .765458 1.72214 0.7842 1.72214
9 552.698 149.756 552.062 139.215 .673468 .171943 3.91681 1.9697 3.91681
10 2241.38 1640.89 2196.62 1654.37 2.25091 1.60456 1.40282 0.4883 1.40282
11 1554.56 1495.41 1526.04 1507.81 1.8044 1.69703 1.06327 0.0885 1.06327
12 594.716 658.778 592.685 663.24 .622596 .735308 .846715 -0.2401 .846715
13 1909.58 3055.86 1872.14 3066.7 1.61595 2.63606 .613019 -0.7060 .613019
14 913.298 836.178 901.59 844.217 1.09862 1.03073 1.06586 0.0920 1.06586
15 2700.29 2641.84 2643.8 2654.16 3.16775 3.35798 .943351 -0.0841 .943351
16 385.244 451.178 390.231 450.283 .536934 .599529 .895593 -0.1591 .895593
17 202.147 195.578 214.767 185.807 .374625 .315903 1.18589 0.2460 1.18589
18 4725.38 3740.99 4626.29 3742.02 4.40622 3.62525 1.21542 0.2815 1.21542
19 4294.47 3871.53 4205.55 3870.56 5.16607 5.19571 .994295 -0.0083 .994295
20 4897.44 4232.47 4794.15 4226.38 7.31014 6.5507 1.11593 0.1582 1.11593

Total number of rows: 346769

Table truncated, full table size 26131 Kbytes.




Supplementary file Size Download File type/resource
GSM417861_MR2625.gpr.gz 13.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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