|
| Status |
Public on Oct 01, 2012 |
| Title |
12353A |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Chaos3 Mammary Tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C3H (C3H/HeNCrl)
genotype/variation: Mcm4Chaos3/Chaos3 ('Chaos3') mouse
gender: female
tissue: Mammary Tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed according to NimbleGen protocols (performed by Cornell CLC)
|
| Label |
Cy5
|
| Label protocol |
Performed according to NimbleGen protocols (performed by Cornell CLC). Five micrograms of genomic DNA from tumor and reference samples were labeled and hybridized to 3x720K mouse Nimblegen CGH whole genome tiling arrays.
|
| |
|
| Channel 2 |
| Source name |
C3H WT Control
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C3H (C3H/HeNCrl)
genotype/variation: WT Control
gender: female
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Performed according to NimbleGen protocols (performed by Cornell CLC)
|
| Label |
Cy3
|
| Label protocol |
Performed according to NimbleGen protocols (performed by Cornell CLC). Five micrograms of genomic DNA from tumor and reference samples were labeled and hybridized to 3x720K mouse Nimblegen CGH whole genome tiling arrays.
|
| |
|
| |
| Hybridization protocol |
Performed according to NimbleGen protocols (performed by Cornell CLC)
|
| Scan protocol |
Scanning was performed in accordance with the NimbleGen protocol (performed by Cornell CLC).
|
| Data processing |
Analyzed with NimbleScan (v2.5)-segmentation algorithm. Copy number changes were identified and segmented with Nimblegen CGH-segMNT algorithm using unaveraged and 10x averaging windows. The significance threshold was set at +/- 0.15 Log2 ratio and required a minimum of two consecutive probes to exhibit change in order to call a segment.
|
| |
|
| Submission date |
Apr 26, 2012 |
| Last update date |
Oct 01, 2012 |
| Contact name |
John Schimenti |
| E-mail(s) |
jcs92@cornell.edu
|
| URL |
http://web.me.com/tcomplex/
|
| Organization name |
Cornell University
|
| Department |
Biomedical Sciences
|
| Lab |
Schimenti
|
| Street address |
T9014A
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL10989 |
| Series (1) |
| GSE37607 |
Spontaneous Nf1 deletion and recurrent copy number alterations in mammary tumorigenesis |
|
