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Sample GSM1841869 Query DataSets for GSM1841869
Status Public on Feb 09, 2017
Title MCF7 rep1
Sample type genomic
 
Source name MCF7 cell line
Organism Homo sapiens
Characteristics gender: female
sample type: cell line
disease state: cancer
cell line: MCF7 cell line
Growth protocol HepG2, SKHep1 and MCF-7 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies). MCF7 cells were cultured with 0.01 mg/ml of insulin (Invitrogen, Carlsbad, California). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen). PC3 and LNCaP were cultured in RPMI1640 media (Gibco, Invitrogen, Life Technologies). All media were supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco).
Extracted molecule genomic DNA
Extraction protocol Cell were resuspended first in cell lysis buffer lysate and incubated with RNAase A (50 U/mg; 30 min; Roche) followed by incubation with proteinase K (20 μl; 20 mg/ml; Roche, Basel, Switzerland) at 55 C for 12 h. Samples were treated and phenol-chloroform (1:1). To precipitate DNA, ethanol [95% (vol/vol)] was added. The pellet was washed and redissolved in buffer DNAse free double distillued water.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol (Cy5 and Cy3)
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol
Scan protocol Standard Illumina procedures using Illumina iScan scanner
Description replicate 1
Data processing Genome Studio (Illumina; version 2011.1, Methylation module (Version 1.9.0)
 
Submission date Jul 31, 2015
Last update date Feb 09, 2017
Contact name David Cheishvili
E-mail(s) david.cheishvili@mcgill.ca
Phone 5143987107
Organization name McGill
Street address ​3655 Sir William Osler
City Montreal
State/province Quebec
ZIP/Postal code H3G 1Y6
Country Canada
 
Platform ID GPL13534
Series (2)
GSE71626 A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness (methylation)
GSE71627 A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness

Data table header descriptions
ID_REF
VALUE Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.1000541 0
cg00000108 0.9540716 0
cg00000109 0.878732 0
cg00000165 0.7858704 0
cg00000236 0.8866822 0
cg00000289 0.7494744 0
cg00000292 0.8236926 0
cg00000321 0.8124356 0
cg00000363 0.9034723 0
cg00000622 0.02479573 0
cg00000658 0.8523153 0
cg00000714 0.09145896 0
cg00000721 0.9437429 0
cg00000734 0.06645709 0
cg00000769 0.02621697 0
cg00000807 0.8947517 0
cg00000884 0.8696806 0
cg00000905 0.07792406 0
cg00000924 0.05397975 0
cg00000948 0.8668016 0

Total number of rows: 485512

Table truncated, full table size 10983 Kbytes.




Supplementary file Size Download File type/resource
GSM1841869_8963303138_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1841869_8963303138_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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