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Sample GSM144679 Query DataSets for GSM144679
Status Public on Nov 18, 2006
Title Madeira_vs_N2
Sample type genomic
 
Channel 1
Source name C. elegans wild isolates JU258
Organism Caenorhabditis elegans
Characteristics Madeira wild strain JU258
Hermaphrodites
whole animals
Extracted molecule genomic DNA
Extraction protocol DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.
Label Cy3
Label protocol Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.
 
Channel 2
Source name C. elegans wild isolate N2
Organism Caenorhabditis elegans
Characteristics Strain N2
Hermaphrodites
whole animals
Extracted molecule genomic DNA
Extraction protocol DNA was prepared either by standard phenol-chloroform extraction followed by ethanol precipitation, or with the Puregene DNA Purification Kit (D-7000A, Gentra Systems) using the solid tissue protocol.
Label Cy5
Label protocol Cy3 and Cy5 dye-labeled random 9mers (TriLink BioTechnologies, Inc.) were diluted to 1 O.D./42 µl of buffer containing 0.125M Tris-HCl (pH 8.0), 0.125M MgCl2, 1.75 µl/ml β-Mercaptoethanol. Mutant DNA samples were labelled with Cy3 and the wild type DNA sample (VC196) was labelled with Cy5. 1 µg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 ºC and then chilled on ice in 0.2 ml PCR tubes. 10 µl of 50X dNTP mixture (1X TE buffer, 10 mM each of dATP, dCTP, dGTP and dTTP), 8 µl DI water and 100 U Klenow fragment (exo-) was added to each tube and mixed well with a pipet. Samples were centrifuged and incubated at 37 ºC for 2 hours. 10 µl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precipitated by adding 11.5 µl 0.5 M NaCl and 110 µl isopropanol, vortexing, incubating in the dark for 10 minutes at room temperature, and centrifuging at 12,000X G for 10 minutes. The supernatant was removed and the DNA pellet was washed with 500 µl 80% ethanol. After centrifugation at 12,000X G for 2 minutes, the supernatant was removed and the pellet was dried in a SpeedVac on low heat for 5 minutes before being rehydrated in 25 µl DI water. DNA concentration was measured using a spectrophotometer.
 
 
Hybridization protocol see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Scan protocol The scanner used was an Axon Scanner (Model # 4000B) .
see Selzer, R.R., T.A. Richmond, N.J. Pofahl, R.D. Green, P.S. Eis, P. Nair, A.R. Brothman, and R.L. Stallings. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
Description NA
Data processing The raw log2 intensity ratio were normalized with the LOESS regression
 
Submission date Nov 15, 2006
Last update date Sep 19, 2007
Contact name Donald Moerman
Organization name University of British Columbia
Department Michael Smith Laboratories
Street address 301 - 2185 East Mall
City Vancouver
State/province British Columbia
ZIP/Postal code V6T 1Z4
Country Canada
 
Platform ID GPL4553
Series (1)
GSE6294 Efficient High-Resolution Discovery in C. elegans by Array Comparative Genomic Hybridization

Data table header descriptions
ID_REF
Log2Intensity Log2Intensity
VALUE Log2Ratio (Cy3/Cy5)

Data table
ID_REF Log2Intensity VALUE
CHR100P00003732 12.0520 0.1457
CHR100P00003819 12.5959 0.0059
CHR100P00003995 10.8447 0.4863
CHR100P00004221 11.8327 -0.0658
CHR100P00004265 11.5954 0.4788
CHR100P00004304 12.5885 0.1337
CHR100P00005199 12.8348 0.1467
CHR100P00005247 11.8619 0.1406
CHR100P00006058 11.8983 0.2509
CHR100P00006104 11.5816 0.0689
CHR100P00006155 9.6534 0.5703
CHR100P00006226 11.9534 0.3656
CHR100P00006266 12.7652 0.1393
CHR100P00008877 11.3573 0.3572
CHR100P00009734 10.2704 0.3337
CHR100P00010045 10.1082 0.6355
CHR100P00010098 10.1705 0.6051
CHR100P00010149 10.8276 0.7588
CHR100P00011518 11.5670 0.3172
CHR100P00011640 11.7461 0.1932

Total number of rows: 384861

Table truncated, full table size 11793 Kbytes.




Supplementary file Size Download File type/resource
GSM144679.txt.gz 12.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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