|
| Status |
Public on Oct 17, 2011 |
| Title |
JB0786_ROMA |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
SKN1
|
| Organism |
Homo sapiens |
| Characteristics |
primary cells: Fibroblasts
gender: male
disease state: normal
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by first homogenizing tissue in lysis buffer and incubating for 60 minutes followed by 3 phenol extractions and precipitation.
|
| 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. (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).
|
| |
|
| Channel 2 |
| Source name |
JB0786
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Ovarian tumor
gender: female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by first homogenizing tissue in lysis buffer and incubating for 60 minutes followed by 3 phenol extractions and precipitation.
|
| 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. (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).
|
| |
|
| |
| 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 (As previously reported Chen, S. et. al. Cancer Biol Ther. 2008 Nov;7(11):1793-802. PMID: 18836286 ).
|
| 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 |
CBS Segmentation Data provided as a supplementary file.
|
| Data processing |
The normalized log ratios from each color reversal experiment were averaged for each segmentation. We then applied the CBS algorithm to this data. The CBS segmentation method is the circular binary segmentation algorithm as described in "Circular binary segmentation for the analysis of array-based DNA copy number data.", Olshen AB, Venkatraman ES, Lucito R, Wigler M., Biostatistics. 2004 Oct;5:557-72 (PMID:15475419).
Seg.mean.txt is the average of normalized log ratios for each experiment.
chrom: Chromosome
loc.start: Chromosome Segment Start Location (1000kb)
loc.end: Chromoseom Segment End Location (1000kb)
num.mark: Number of Markers in the Segment
seg.mean: The Segment Mean
|
| |
|
| Submission date |
Mar 17, 2011 |
| Last update date |
Oct 17, 2011 |
| Contact name |
Kazimierz O. Wrzeszczynski |
| E-mail(s) |
[email protected]
|
| Phone |
516-367-8395
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Lab |
Rob Luctio
|
| Street address |
One Bungtown Rd.
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL8581 |
| Series (2) |
| GSE28013 |
Representational Oligonucleotide Microarray Analysis (ROMA) array for Copy Number Variation Detection. |
| GSE28015 |
Identification of Tumor Suppressors and Oncogenes from Genomic and Epigenetic Features in Ovarian Cancer |
|
| Data table header descriptions |
| ID_REF |
|
| F635.MEDIAN |
Mean of pixel values for each spot scanned at 635nm wavelength |
| F532.MEDIAN |
Mean of pixel values for each spot scanned at 532nm wavelength |
| LOWRED |
Lowess normalized value for each spot in red colour |
| LOWGREEN |
Lowess normalized value for each spot in green colour |
| LOCAL.RED |
Local normalized output for each spot in red |
| LOCAL.GREEN |
Local normalized output for each spot in green |
| VALUE |
log ratio of the two local normalized values for each probe (tumor/reference) |
