|
| Status |
Public on Jan 01, 2016 |
| Title |
NCI-HPN-F2K Colon p65 Transformed |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
mouse colon epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Stage: p65
gender: female
|
| Growth protocol |
The epithelial cells were grown in DMEM/F12 media supplemented with low fetal bovine serum (2-5%).The cells were fed every 10 days to promote in vitro cellular transformation (Padilla Nash et al., 2012).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the murine epithelial cells and the mouse C57BL/6 liver cells (normal reference DNA) using protocols described in http://www.riedlab.nci.nih.gov/protocols.
|
| Label |
Cy3
|
| Label protocol |
7ug of digested DNA was prepared for labeling with the BioPrime Array Genomic Labeling Kit using Cy3 -dUTP for the test DNA and Cy5-dUTP for the reference DNAas described in Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol.
|
| |
|
| Channel 2 |
| Source name |
Male Mouse DNA
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: mouse liver cells
|
| Growth protocol |
The epithelial cells were grown in DMEM/F12 media supplemented with low fetal bovine serum (2-5%).The cells were fed every 10 days to promote in vitro cellular transformation (Padilla Nash et al., 2012).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from the murine epithelial cells and the mouse C57BL/6 liver cells (normal reference DNA) using protocols described in http://www.riedlab.nci.nih.gov/protocols.
|
| Label |
Cy5
|
| Label protocol |
7ug of digested DNA was prepared for labeling with the BioPrime Array Genomic Labeling Kit using Cy3 -dUTP for the test DNA and Cy5-dUTP for the reference DNAas described in Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol.
|
| |
|
| |
| Hybridization protocol |
The differentially labeled targets sample and reference DNA were combined with Agilent 10X Blocking Agent, Agilent 2X Hybridization Buffer, and Cot-1 DNA , denatured at 95°C for 3 min and preannealed for 30 min at 37°C according to the Agilent Oligonucleotide Array-Based CGH for Genomic Analysis Protocol. The denatured probe was applied to the Agilent Mouse Genome CGH 244K Microarray Kit according to the manufacturer's instructions.
|
| Scan protocol |
The arrays were scanned using an Agilent Scanner System. Images were quantified using Agilent Feature Extraction Software (version 8.1.1).
|
| Description |
female
|
| Data processing |
Rank Segmentation algorithm of Nexus Copy Number 6 was used to analyze aCGH data. Significance Threshold: 5E-6; Max Contiguous Probe Spacing: 3000; Min number of probes per segment: 10; Systematic correction: linear correction with correction file provided by Nexus.
|
| |
|
| Submission date |
Jul 10, 2015 |
| Last update date |
Jan 01, 2016 |
| Contact name |
Hesed Maria Padilla-Nash |
| E-mail(s) |
nashh@mail.nih.gov
|
| Phone |
301-435-4019
|
| Organization name |
NCI
|
| Department |
Genetics Branch
|
| Lab |
Section of Cancer Genomics
|
| Street address |
50 South Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-8010 |
| Country |
USA |
| |
|
| Platform ID |
GPL15076 |
| Series (2) |
| GSE70790 |
Molecular Characterization of Spontaneously Transformed Epithelial Murine Colon Cell Lines as a Model of Human Colorectal Neoplasia (CGH) |
| GSE72349 |
Molecular Characterization of Spontaneously Transformed Epithelial Murine Colon Cell Lines as a Model of Human Colorectal Neoplasia |
|
