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Sample GSM1818744 Query DataSets for GSM1818744
Status Public on Jan 01, 2016
Title NCI-HPN-F1K Colon p51 Transformed
Sample type genomic
 
Channel 1
Source name mouse colon epithelial cells
Organism Mus musculus
Characteristics strain: C57BL/6
Stage: p51
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

Data table header descriptions
ID_REF
VALUE log2 ratio (test/reference) representing copy number of segment

Data table
ID_REF VALUE
A_67_P04000012 0.1078
A_67_P04000019 0.1078
A_67_P04000027 0.1078
A_67_P04000032 0.1078
A_67_P04000058 0.1078
A_67_P04000065 0.1078
A_67_P04000071 0.1078
A_67_P04000083 0.1078
A_67_P04000100 0.1078
A_67_P04000126 0.1078
A_67_P04000143 0.1078
A_67_P00000082 0.1078
A_67_P04000179 0.1078
A_67_P04000184 0.1078
A_67_P04000193 0.1078
A_67_P04000207 0.1078
A_67_P00000133 0.1078
A_67_P00000149 0.1078
A_67_P04000256 0.1078
A_67_P00000176 0.1078

Total number of rows: 233970

Table truncated, full table size 5053 Kbytes.




Supplementary file Size Download File type/resource
GSM1818744_US45102909_251469512430_S01_CGH_105_Dec08.txt.gz 74.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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