|
| Status |
Public on Sep 14, 2016 |
| Title |
Chaos3/Chaos3 C3H Congenic |
| Sample type |
mixed |
| |
|
| Channel 1 |
| Source name |
mammary tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: Chaos3/Chaos3 C3H Congenic
genotype/variation: MCM4Chaos3/Chaos3 point mutation
gender: female
tissue: mammary tumor
# of cnvs: 73
|
| Growth protocol |
Tumors developed spontaneously within female mice with the MCM4Chaos3/Chaos3 point mutation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from primary tumors by solubilizing in lysis buffer (50 mMTris-HCl pH 8.0; 100 mM EDTA pH 8.0; 100 mM NaCl; 1% SDS; 0.5 mg/ml ProteinaseK) for 3 hours at 55°, phenol/chloroform extraction, precipitation of the DNA in 0.8 volumes isopropanol, followed by spooling and washes in 70% then 100% ethanol.
|
| Label |
cy5
|
| Label protocol |
Manufacterer's protocol
|
| |
|
| Channel 2 |
| Source name |
reference wild-type DNAs from C57Bl/6J and C3HeB/FeJ
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J and C3HeB/FeJ
genotype/variation: wild type
sample type: reference DNA
|
| Growth protocol |
Tumors developed spontaneously within female mice with the MCM4Chaos3/Chaos3 point mutation
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from primary tumors by solubilizing in lysis buffer (50 mMTris-HCl pH 8.0; 100 mM EDTA pH 8.0; 100 mM NaCl; 1% SDS; 0.5 mg/ml ProteinaseK) for 3 hours at 55°, phenol/chloroform extraction, precipitation of the DNA in 0.8 volumes isopropanol, followed by spooling and washes in 70% then 100% ethanol.
|
| Label |
cy3
|
| Label protocol |
Manufacterer's protocol
|
| |
|
| |
| Hybridization protocol |
Manufacterer's protocol
|
| Scan protocol |
Images were scanned using Agilent’s SureScan Microarray Scanner
|
| Description |
20892
US83000170_252741411072_S01_CGH_107_Sep09
|
| Data processing |
Agilent’s Cytogenomics software was used for spot identification and signal quantification, following default Linear and LOWESS normalization of test/reference ratios and background correction.
Criteria for calling amplifications/deletions were as follows: minimum number of contiguous probes >= 3, minimum avg. absolute log2 ratio >= 0.25.
|
| |
|
| Submission date |
May 26, 2016 |
| Last update date |
Sep 14, 2016 |
| Contact name |
John Schimenti |
| E-mail(s) |
jcs92@cornell.edu
|
| Phone |
607-253-3636
|
| Organization name |
Cornell University
|
| Department |
Biomedical Scinces
|
| Lab |
14853
|
| Street address |
College of Veterinary Medicine T9014A
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL10448 |
| Series (1) |
| GSE81967 |
Mouse tumors: Chaos3 Mammary Tumors (MTs) vs. Controls |
|
