|
| Status |
Public on Mar 13, 2008 |
| Title |
DNA from T31 Cell Line 56 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
DNA from T31 Cell Line 56
|
| Organisms |
Cricetulus griseus; Mus musculus |
| Characteristics |
Radiation Hybrid Cell Line
|
| Growth protocol |
RH and A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent. Harvested by trypsinization, then pelleting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen Dneasy Tissue kit according to the manufacturer's instructions
|
| Label |
cy5
|
| Label protocol |
The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5/cy3 labeled dUTP.
|
| |
|
| Channel 2 |
| Source name |
A23 Hamster Cell Line
|
| Organism |
Cricetulus griseus |
| Characteristics |
Hamster fibroblast cell line
|
| Growth protocol |
RH and A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent. Harvested by trypsinization, then pelleting.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Qiagen Dneasy Tissue kit according to the manufacturer's instructions
|
| Label |
cy3
|
| Label protocol |
The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating cy5/cy3 labeled dUTP.
|
| |
|
| |
| Hybridization protocol |
The samples were hybridized for 40 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.
|
| Description |
none
|
| Data processing |
The CGH data were normalized as follows. First, the data for each array were subtracted by its own individual mode (a CGH value corresponding to the primary peak). This gave the primary mode for each array a log10(RH/A23) copy number ratio of zero. In the next step, the CGH data was pooled over all arrays and the primary and second modes estimated by modeling the data as a mixture of two Gaussian distributions 4. Because extra copy regions in the autosomes represent three copies (one mouse and two hamster copies) compared to two (two hamster copies), the data for the autosomes was multiplied by a common scaling factor of (log10[3/2])/(secondary mode CGH value - primary mode CGH value). Consequently, the normalized CGH data for the autosomes had a primary mode at log10(2 copies/2 copies) = 0 and a secondary mode at log10(3 copies/2 copies) = 0.176. Since extra copy regions on the X chromosome represent two copies (one mouse plus one hamster) compared to one (one hamster copy), the data for the X chromosome was multiplied by log10(2/1)/(secondary mode CGH value - primary mode CGH value), giving a secondary mode at log10(2 copies/1 copy) = 0.301.
|
| |
|
| Submission date |
Sep 14, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Christopher Park |
| Phone |
310-948-7917
|
| Organization name |
UCLA
|
| Department |
Molecular and Medical Pharmacology
|
| Lab |
Desmond Smith
|
| Street address |
23-151 CHS, 650 Charles E. Young Drive
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL4092 |
| Series (2) |
| GSE9041 |
Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids Ib |
| GSE9052 |
Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids |
|
