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Sample GSM2579236 Query DataSets for GSM2579236
Status Public on Oct 31, 2017
Title PMC42-ET Control Rep 1
Sample type genomic
 
Source name Cell line, PMC42-ET Untreated
Organism Homo sapiens
Characteristics cell line: PMC42-ET
Treatment protocol EGF treatment was performed on cultures by supplementing EGF at 10ng/ml for 72 hours prior to harvesting
Growth protocol Both PMC42-ET and the PMC42-LA sublines were grown in RPMI, supplemented with 10% FCS and penicillin/streptomycin, at 370C/10% CO2.
Extracted molecule genomic DNA
Extraction protocol cells were washed with 1 x PBS, dispersed by trypsin digestion, and the cell pellets were lysed in RIPA buffer. Lysates where then digested with proteinase K, followed by phenol-chloroform extraction and isopropanol precipitation
Label Cy5 and Cy3
Label protocol As per Illumina protocol
 
Hybridization protocol As per Illumina protocol
Scan protocol As per Illumina protocol
Description ETC1
Data processing Data analysed using R and Bioconductor with the ChAMP Library v2.6.0
 
Submission date Apr 16, 2017
Last update date Oct 31, 2017
Contact name Nicholas C Wong
E-mail(s) nick.wong@monash.edu
Organization name Monash University
Department Monash Bioinformatics Platform, Central Clinical School
Street address Wellington Road
City Clayton
State/province Victoria
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL13534
Series (1)
GSE97853 DNA methylation profile of model breast cancer cell lines PMC42-ET and PMC42-LA

Data table header descriptions
ID_REF
VALUE Average Beta or normalized (provide the normalization method) Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00050873 0.549668874 0
cg00212031 0.3926097 0
cg00213748 0.677333333 0
cg00214611 0.75136612 0
cg00455876 0.183098592 0
cg01707559 0.327385892 0
cg02004872 0.292164675 0
cg02011394 0.553846154 0
cg02050847 0.459244533 0
cg02233190 0.41884058 0
cg02494853 0.363786366 0
cg02839557 0.512195122 0
cg02842889 0.435736677 0
cg03052502 0.535714286 0
cg03155755 0.441558442 0
cg03244189 0.486040609 0
cg03443143 0.495708155 0
cg03683899 0.450881612 0
cg03695421 0.377570093 0
cg03706273 0.033111323 0

Total number of rows: 485512

Table truncated, full table size 11750 Kbytes.




Supplementary file Size Download File type/resource
GSM2579236_6264509002_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM2579236_6264509002_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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