|
| Status |
Public on Oct 28, 2007 |
| Title |
B6NSim.vs.B6J_hyb1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Genomic DNA isolated from the liver of a C57BL/6NSim inbred mouse
|
| Organism |
Mus musculus |
| Characteristics |
DNA prep ID: C57BL/NSim-L
Strain: C57BL/Nsim
Tissue: liver
Age: 4-8 weeks
Gender: Female
|
| Biomaterial provider |
Simonsen Laboratories, Inc.
|
| Growth protocol |
Wild-type mice were maintained on a standard laboratory diet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.
|
| Label |
Cy5
|
| Label protocol |
1 ug of DNA was sonicated to a size range of 500-2000 bp, denatured at 98°C with Cy3 or Cy5 labeled random nonamer (TriLink Biotechnologies), chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each, Invitrogen) for 2 hr at 37°C. End products were precipitated with isopropanol and resuspended in water.
|
| |
|
| Channel 2 |
| Source name |
Genomic DNA isolated from the liver of a C57BL/6J inbred mouse
|
| Organism |
Mus musculus |
| Characteristics |
DNA prep ID: C57BL/6J-L
Strain: C57BL/6J
Tissue: liver
Age: 7 months
Gender: Female
|
| Biomaterial provider |
The Jackson Laboratory
|
| Growth protocol |
Wild-type mice were maintained on a standard laboratory diet
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications: livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. Two additional extrections were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.
|
| Label |
Cy3
|
| Label protocol |
1 ug of DNA was sonicated to a size range of 500-2000 bp, denatured at 98°C with Cy3 or Cy5 labeled random nonamer (TriLink Biotechnologies), chilled on ice, and incubated with 100 units Klenow fragment (NEB) and dNTP mix (6 mM each, Invitrogen) for 2 hr at 37°C. End products were precipitated with isopropanol and resuspended in water.
|
| |
|
| |
| Hybridization protocol |
Hybridizations were carried out for 18 hr at 42°C using the Maui Hybridization System (BioMicro Systems). Arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) .
|
| Scan protocol |
Microarrays were scanned with an Axon GenePix 4000B scanner with pixel size set to 5um. GenePix Pro 4.0 software was used for gridding and quantitation of intensities.
|
| Description |
none
|
| Data processing |
Signal intensities were normalized using the normalize.qspline method from the affy Bioconductor package.
|
| |
|
| Submission date |
Aug 27, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Ira M Hall |
| E-mail(s) |
hall@cshl.edu
|
| Phone |
516-287-3764
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Lab |
Hall
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL5777 |
| Series (1) |
| GSE8885 |
Recurrent DNA copy number variation in the laboratory mouse |
|
