|
| Status |
Public on May 08, 2007 |
| Title |
Ankle, NOS, Melanoma, NOS (12735484) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
TB1100DF1X10
|
| Organism |
Homo sapiens |
| Characteristics |
Cell Line WM 3211
TB1100DF1X10
|
| Growth protocol |
"Ankle, NOS"; Melanoma, NOS
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
|
| Label |
Cy3
|
| Label protocol |
One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
|
| |
|
| Channel 2 |
| Source name |
pooled reference
|
| Organism |
Homo sapiens |
| Characteristics |
pooled reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from frozen tumors or cultured cells by overnight digestion, phenol-chloroform extraction and ethanol precipitation.
|
| Label |
Cy5
|
| Label protocol |
One µg of tumor and reference DNA were labeled with Cy3 or Cy5, respectively (Amersham, Piscataway, NJ) using the BioPrime random-primed labeling kit (Invitrogen, Carlsbad, CA). Labeled tumor and reference DNA were combined and precipitated with human Cot-1 DNA to reduce non-specific binding.
|
| |
|
| |
| Hybridization protocol |
DNA was resuspended and hybridized to the array for 72h at 37oC on a rotating platform. Additional details are found in: Greshock, J, Naylor, TL, Margolin, A, et al. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res 2004; 14: 179-87
|
| Scan protocol |
Images were scanned with an Axon 4500 microarray scanner (Axon, Union City, CA) and analyzed with GenePix 3.0 software (Axon).
|
| Description |
"Ankle, NOS"; Melanoma, NOS; University of Pennsylvania; 10/24/2003
|
| Data processing |
All spots were subjected to a pin-tip normalization.
|
| |
|
| Submission date |
Apr 27, 2007 |
| Last update date |
May 07, 2007 |
| Contact name |
Joel Greshock |
| Organization name |
GlaxoSmithKline
|
| Department |
Translational Medicine, Oncology
|
| Street address |
2301 Renaissance Blvd.
|
| City |
King of Prussia |
| State/province |
PA |
| ZIP/Postal code |
19406 |
| Country |
USA |
| |
|
| Platform ID |
GPL4894 |
| Series (1) |
| GSE7692 |
Cancer cell lines as genetic models of their parent histology: analyses based on array comparative genomic hybridization |
|
| Data table header descriptions |
| ID_REF |
|
| SLIDE |
Slide/Exeriment Identifier |
| Dia |
Spot Diameter in Pixels |
| F635_Median |
Median foreground measurement of Cy5 channel |
| F635_Mean |
Mean foreground measurement of Cy5 channel |
| F635_SD |
Standard Deviation of foreground measurement of Cy5 channel |
| B635_Median |
Median background of Cy5 channel |
| B635_Mean |
Mean background of Cy5 channel |
| B635_SD |
Standard deviation of background of Cy5 channel |
| PCT_GT_B635_1SD |
Percent of pixels > 1 standard deviation above background for Cy5 channel |
| PCT_GT_B635_2SD |
Percent of pixels > 2 standard deviation above background for Cy5 channel |
| F635_PCT_Sat |
Percent of pixels that are saturated for Cy5 channel |
| F532_Median |
Median foreground measurement of Cy3 channel |
| F532_Mean |
Mean foreground measurement of Cy3 channel |
| F532_SD |
Standard Deviation of foreground measurement of Cy3 channel |
| B532_Median |
Median background of Cy3 channel |
| B532_Mean |
Mean background of Cy3 channel |
| B532_SD |
Standard deviation of background of Cy3 channel |
| PCT_GT_B532_1SD |
Percent of pixels > 1 standard deviation above background for Cy5 channel |
| PCT_GT_B532_2SD |
Percent of pixels > 2 standard deviation above background for Cy5 channel |
| F532_PCT_Sat |
Percent of pixels that are saturated for Cy3 channel |
| Ratio_of_Medians_532_635 |
Ratio of median pixel values (Cy3/Cy5) |
| Ratio_of_Means_532_635 |
Ratio of mean pixel values (Cy3/Cy5) |
| Median_of_Ratios_532_635 |
Median of all individual pixel ratios (Cy3/Cy5) |
| Mean_of_Ratios_532_635 |
Mean of all individual pixel ratios (Cy3/Cy5) |
| Ratios_SD_532_635 |
Standard deviation of all individual pixel ratios (Cy3/Cy5) |
| Rgn_Ratio_532_635 |
Red to green ratio |
| Rgn_R2_532_635 |
Red to green correlation |
| F_Pixels |
The number of pixels analyzed as foreground (both Cy3 and Cy5 uses same exact pixels) |
| B_Pixels |
The number of pixels analyzed as background (same for Cy3 and Cy5) |
| Sum_of_Medians |
Sum of Pixel intensity medians |
| Sum_of_Means |
Sum of Pixel intensity means |
| Log_Ratio_532_635 |
Log base 2 of the Cy3/Cy5 ratio |
| F635_Median_B635 |
Median Foreground intensity minus Background intensity, Cy5 channel |
| F532_Median_B532 |
Median Foreground intensity minus Background intensity, Cy3 channel |
| F635_Mean_B635 |
Mean Foreground intensity minus Background intensity, Cy5 channel |
| F532_Mean_B532 |
Mean Foreground intensity minus Background intensity, Cy3 channel |
| Ratio_Median |
Median Cy3/Cy5 ratio (using the Background corrected ratio of medians) for that specific print tip |
| Cy3_corrected |
Adjusted background corrected intensity (by print tip)= F532_Median_B532 / Ratio_Median_Tip |
| VALUE |
log(GREENsignal/REDsignal) per feature (processed signals used). |
| A |
mean log intensity |
| Sig_var_mean_Cy3 |
Signal variation from mean intsity for Cy3 channel |
| Sig_var_mean_Cy5 |
Signal variation from mean intsity for Cy5 channel |
| Mean_med_corr_Cy3 |
Mean-Median correlation for Cy3 channel |
| Mean_med_corr_Cy5 |
Mean-Median correlation for Cy5 channel |
