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Sample GSM3037805 Query DataSets for GSM3037805
Status Public on Mar 13, 2018
Title MDA-MB-231_HM.LNm5_1
Sample type genomic
 
Source name cell line
Organism Homo sapiens
Characteristics cell line: MDA-MB-231_HM.LNm5
cell type: breast cancer cell line
gfp: no fluorescent proteins
Treatment protocol Untreated cells
Growth protocol Cells grown in DMEM 10% FBS, 1% P/S
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was made using Qiagen DNA mini kit and concentration determined using a Nanodrop Spectrophotometer
Label Cy5/Cy3
Label protocol Bisulfite conversion of genomic DNA samples was performed using the Zymo EZ DNA Methylation kit. 200ng of bisulfite-converted DNA was then prepared for hybridisation according to the Illumina Infinium HD Assay Methylation Protocol Guide.
 
Hybridization protocol Samples were hybridised to Illumina MethylationEPIC arrays for 17 hours at 48°C in an Illumina Hybridisation Oven. Single base extension and staining were performed as per the Illumina Infinium HD Protocol.
Scan protocol Slides were scanned using an Illumina HiScan.
Description SAMPLE 4
Data processing Genomic DNA extracted from cell lines was genotyped using Infinium HumanCytoSNP-12 v2.1 BeadChip arrays (Illumina)
 
Submission date Mar 12, 2018
Last update date Mar 13, 2018
Contact name Andrew Pattison
E-mail(s) andrew.pattison@monash.edu
Organization name Monash University
Street address Wellington Rd
City Melbourne
State/province Vic
ZIP/Postal code 3800
Country Australia
 
Platform ID GPL13829
Series (2)
GSE111705 Functional and genomic characterization of a xenograft model system for the study of metastasis in triple-negative breast cancer
GSE111706 Metastasis in triple-negative breast cancer

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
cnvi0111185 NC 0 0.9759056 1.38585 1 0.04280609
cnvi0111186 NC 0 0.0327662 0.3265693 0.002644949 0.2537925
cnvi0111187 NC 0 0.9832007 1.759426 1 0.0306641
cnvi0111188 NC 0 0.0127962 1.275569 0.001681746 0.03639683
cnvi0111189 NC 0 0.02098606 1.485405 0 -0.0100641
cnvi0111192 NC 0 0.01810927 1.149176 0 0.1421745
cnvi0111193 NC 0 0.002938946 1.457655 0 0.0336569
cnvi0111194 NC 0 0.9845238 1.376673 1 0.02032637
cnvi0111195 NC 0 0.0301102 1.827754 0 -0.2027633
cnvi0111197 NC 0 0.01904932 0.7606632 0 0.06265144
cnvi0111198 NC 0 0.9642249 1.223812 0.9941591 -0.122383
cnvi0111199 NC 0 0.02476091 1.173052 0 -0.003775311
cnvi0111200 NC 0 0.9875091 0.9376279 0.9996846 0.0756577
cnvi0111201 NC 0 0.0210791 1.096395 0.004362121 -0.001459151
cnvi0111202 NC 0 0.9220883 1.319947 0.993166 0.03150956
cnvi0111203 NC 0 0.04024561 2.126385 0 0.1080367
cnvi0111204 NC 0 0.9934419 1.373732 1 0.1834591
cnvi0111205 NC 0 0.7931527 0.9243079 0.9702829 -0.0142086
cnvi0111206 NC 0 0.006673756 0.7724624 0.000997823 0.1695354
cnvi0111207 NC 0 0.9904358 0.7732242 1 0.083504

Total number of rows: 294602

Table truncated, full table size 17292 Kbytes.




Supplementary file Size Download File type/resource
GSM3037805_202066280019_R04C01_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM3037805_202066280019_R04C01_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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