|
| Status |
Public on Jun 15, 2016 |
| Title |
D2A1 cells_Rep1 |
| Sample type |
genomic |
| |
|
| Source name |
Mouse mammary tumor-derived cell line D2A1
|
| Organism |
Mus musculus |
| Characteristics |
cell line: D2A1
mouse strain: BALB/c
cell line origin: Spontaneous mammary tumor
malignancy status: Malignant
metastatic ability: High
|
| Treatment protocol |
None
|
| Growth protocol |
Cells were cultured in their recommended growth media using standard procedures
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA-free DNA was prepared from the cell lines using the Gentra Puregene Cell Kit (Qiagen) according to manufacturer's protocol and resuspended in low EDTA TE buffer. DNA quantity was assessed using PicoGreen fluorometry and integrity was assessed by agarose gel electrophoresis. Qualified gDNA samples were normalized to 50ng/ul.
|
| Label |
Biotin
|
| Label protocol |
The Affymetrix SNP 6.0 protocol was used. gDNA was subjected to spearate restriction enzyme digestions using Sty1 and Nsp. For each digest reaction (2/sample) restriction products were ligated to a common adaptor and amplifed by PCR. The amplified reaction products for each sample were pooled, purified and then fragmented. Fragmented PCR amplicons were end-labeled using terminal deoxynucleotidyl transferase with the Biotin-labled GeneChip DNA Labeling Reagent.
|
| |
|
| Hybridization protocol |
Samples were hybridized to the arrays at 50oC for 16-18 hours
|
| Scan protocol |
Washing and staining of the hydridized array was performed using the Affymetrix 450 fluidics station, and arrays were scanned using the Affymetrix GeneChip 3000 7G Plus scanner
|
| Description |
Copy number variation data
|
| Data processing |
Array images and intensity data were collected using the Affymetrix GEneChip Command Console (AGCC) Software. Array data were analyzed using the R package MouseDivGeno. Data from normal tissue of matched mouse strains were used as references to identify regions of copy number gain or loss.
The 27 mouse tumor cell lines were assayed by the Mouse Diversity Genotyping array, a Affymetrix mouse genotyping array similar to human SNP 6.0. The array were analyzed by using the R package MouseDivGeno. Copy number analysis was performed using data from normal DNA of matched mouse strains as references for copy number inference. Reference set can be downloaded from http://cgd.jax.org/datasets/diversityarray/CELfiles.shtml.
|
| |
|
| Submission date |
Jun 15, 2015 |
| Last update date |
Jun 15, 2016 |
| Contact name |
Maxwell Lee |
| E-mail(s) |
leemax@mail.nih.gov
|
| Phone |
240-276-5239
|
| Organization name |
National Cancer Institute, NIH
|
| Department |
CCR
|
| Lab |
Laboratory of Human Carcinogenesis
|
| Street address |
Building 37, Room 5120
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL13147 |
| Series (1) |
| GSE69902 |
Copy number variation data in malignant mouse mammary cell lines |
|
