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Sample GSM144676 Query DataSets for GSM144676
Status Public on Nov 18, 2006
Title gk488_vs_N2
Sample type genomic
 
Channel 1
Source name C. elegans mutant gk488
Organism Caenorhabditis elegans
Characteristics Strain gk488
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 GPL4552
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
CHR200P00000577 10.8288 -0.0111
CHR200P00000789 11.6196 0.4880
CHR200P00000879 10.8878 -0.2177
CHR200P00000966 9.9143 0.2280
CHR200P00001100 9.8871 0.6536
CHR200P00001270 11.6040 0.2410
CHR200P00001357 10.2439 0.0395
CHR200P00001552 12.2218 0.1085
CHR200P00001646 10.1474 0.2278
CHR200P00001764 10.2819 0.0860
CHR200P00001864 10.9661 0.1845
CHR200P00001930 9.5236 0.1738
CHR200P00002032 10.9791 -0.1163
CHR200P00002121 11.1669 0.1271
CHR200P00002404 9.4839 -0.0440
CHR200P00002508 10.6609 0.3539
CHR200P00002514 11.3364 0.0660
CHR200P00002520 11.4323 0.0507
CHR200P00002526 11.1763 0.0153
CHR200P00002533 10.8559 0.2547

Total number of rows: 380187

Table truncated, full table size 11667 Kbytes.




Supplementary file Size Download File type/resource
GSM144676.txt.gz 11.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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