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Sample GSM3084305 Query DataSets for GSM3084305
Status Public on Apr 07, 2018
Title gDNA-100B_409_2-vs-PreMA
Sample type genomic
 
Channel 1
Source name PreMA gDNA from ancestral population
Organism Caenorhabditis elegans
Characteristics population: Ancestral
generations: 0
individual: 1
sample: final
Treatment protocol This is the ancestral control line. It was cryogenically frozen at −86°C throughout the MA period of the other lines.
Growth protocol The population was grown on NGM plates (Nematode Growth Medium) at 20˚C and maintained on 90x15 mm petri dishes seeded with 750μl of Escherichia coli (OP50) in YT medium.
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 solid tissue protocol.
Label Cy5
Label protocol Cy3/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. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C 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 mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated 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 centrfuging 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. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)
 
Channel 2
Source name 100B_409_2 gDNA from populations
Organism Caenorhabditis elegans
Characteristics population: 100B
generations: 409
individual: 2
sample: final
Treatment protocol Spontaneous mutation accumulation via population bottlenecks of N = 100 every generation.
Growth protocol The population was grown on NGM plates (Nematode Growth Medium) at 20˚C and maintained on 90x15 mm petri dishes seeded with 750μl of Escherichia coli (OP50) in YT medium.
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 solid tissue protocol.
Label Cy3
Label protocol Cy3/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. 1 μg of genomic DNA was added to each random 9mer buffer solution, denatured at 95 °C 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 mixede well with a pipet. Samples were centrifuged and incubated at 37 °C for 2 hours. 10 μl 0.5 M EDTA was added and mixed well to stop the labeling reaction. DNA was precpitated 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 centrfuging 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. See Maydan JS, Lorch A, Edgley ML, Flibotte S, and Moerman DG. 2010. Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. BMC Genomics Jan 25;11:62 (PMID: 20100350)
 
 
Hybridization protocol The sample was rehydrated in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems, Inc.), denatured at 95 °C for 5 min, and then cooled to 42 °C. Hybridizations were carried out for 18 hr at 42 °C in the NimbleGen Service Laboratory. The arrays were washed using a NimbleGen Wash Buffer System (NimbleGen Systems, Inc.) and immediately dried down by centrifugation. 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 (PMID 16075461).
Scan protocol The scanner used was an Axon Scanner (Model # 40008). 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 (PMID 16075461).
Description Genome variation profiling by genome tiling array
Data processing The raw log2 intensity ratios were normalized with the LOESS regression.
 
Submission date Apr 06, 2018
Last update date Apr 07, 2018
Contact name Vaishali Katju
E-mail(s) vkatju@cvm.tamu.edu
Phone 9794581036
Organization name Texas A&M University
Department Veterinary Integrative Bioscience
Street address Veterinary Integrative Bioscience, MS 4458
City College Station
State/province Texas
ZIP/Postal code 77843
Country USA
 
Platform ID GPL20029
Series (1)
GSE112821 Mutational and Transcriptional Landscape of Spontaneous Gene Duplications and Deletions in Caenorhabditis elegans

Data table header descriptions
ID_REF
VALUE log2 transformed test/control ratios

Data table
ID_REF VALUE
CHR100P00000503 -0.364
CHR100P00000512 -0.3128
CHR100P00000519 -0.2522
CHR100P00000527 -0.3156
CHR100P00000533 -0.3187
CHR100P00001257 0.2891
CHR100P00001285 -0.1052
CHR100P00001318 0.5372
CHR100P00001367 0.8075
CHR100P00001376 0.4523
CHR100P00001381 0.6579
CHR100P00001386 0.4161
CHR100P00003652 -0.0411
CHR100P00003758 0.2116
CHR100P00003811 -0.342
CHR100P00003816 -0.1134
CHR100P00003822 -0.0771
CHR100P00003827 -0.3307
CHR100P00003833 -0.421
CHR100P00003994 -0.5029

Total number of rows: 719981

Table truncated, full table size 16444 Kbytes.




Supplementary file Size Download File type/resource
GSM3084305_542416_A03_2012-11-12_532.pair.gz 11.8 Mb (ftp)(http) PAIR
GSM3084305_542416_A03_2012-11-12_635.pair.gz 11.8 Mb (ftp)(http) PAIR
Processed data included within Sample table

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