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Sample GSM1380707 Query DataSets for GSM1380707
Status Public on May 08, 2014
Title genomic dna from ovarian_OVKATE_d3_Aza
Sample type genomic
 
Source name ovarian_OVKATE_Aza
Organism Homo sapiens
Characteristics cell line: OVKATE
cell type: ovarian cancer cell line
sample group: D3_Aza
Treatment protocol Cell lines were treated with 500 nM 5-azacitidine for 72 hours while in log-growth phase, changing the media and drug every 24 hours for AZA treatment. Cells were harvested at 1, 3, 7, 10, 14, or 21 days following initial application of drug.
Growth protocol Breast, colon, and ovarian cancer cell lines were maintained under ATCC recommended growth conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted and purified from cell pellets using the Qiagen DNeasy Kit according to the manufacturer's instructions.
Label Cy5 and Cy3
Label protocol Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.
 
Hybridization protocol Bisulfite-converted DNA was analyzed using Illumina’s Infinium Human Methylation450 Beadchip Kit (WG-314-1001) by following manufacturer’s manual. Beadchip contains 485,577 CpG loci in human genome. Briefly, 4 ul of bisulfite-converted DNA was added to a 0.8 ml 96-well storage plate (Thermo Scientific), denatured in 0.014N sodium hydroxide, neutralized and amplified with kit-provided reagents and buffer at 37C for 20-24 hours. Samples were fragmented using kit-provided reagents and buffer at 37C for one hour and precipitated by adding 2-propanol. Re-suspended samples were denatured in a 96-well plate heat block at 95C for 20 minutes. 12 ul of each sample was loaded onto a 12-sample chip and the chips were assembled into hybridization chamber as instructed in the manual. After incubation at 48C for 16-20 hours, chips were briefly washed and then assembled and placed in a fluid flow-through station for primer-extension and staining procedures.
Scan protocol Polymer-coated chips were image-processed in Illumina’s iScan scanner.
Data processing Data were extracted using Methylation Module of GenomeStudio v1.0 Software. The 'signal_intensities.txt' contains unmethylated and methylated signal intensities. Methylation status of each CpG site was presented as b (beta) value based on following definition:
b value = (signal intensity of methylation-detection probe)/(signal intensity of methylation- detection probe + signal intensity of non-methylation-detection probe + 100).
 
Submission date May 06, 2014
Last update date May 08, 2014
Contact name Stephen Baylin
E-mail(s) sbaylin@jhmi.edu
Phone 4109558506
Organization name Johns Hopkins UniversityJohns Hopkins Medical Institutions
Department Oncology
Street address 1650 Orleans St CRB I RM 541
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
Platform ID GPL13534
Series (2)
GSE57342 Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers [methylation]
GSE57343 Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers

Supplementary data files not provided
Processed data are available on Series record

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