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Sample GSM1547538 Query DataSets for GSM1547538
Status Public on Dec 31, 2015
Title HMEC TGFb 12 d Sss I
Sample type genomic
 
Source name Human mammary epithelial cell TGFb treated 12 d, M. Sss I treat
Organism Homo sapiens
Characteristics cell line: HMLE
time point: 12d
Treatment protocol To induce the expression of Twist, HMLE-Twist-ER cells were exposed to 4-hydroxy tamoxifen (4-OHT) at a concentration of 20 nM continuously until change in morphology was observed, typically 12 days. TGF-beta1 at a concentration of 2.5 ng/ml was used to treat HMLE cells for 12 days.
Growth protocol The immortalized human mammary epithelial cell line (HMLE) and the derivative cell line HMLE-Twist-ER were kindly provided by the Robert Weinberg laboratory (MIT). The culture of the cells was carried out as described previously (Elenbaas et al., 2001; Mani et al., 2008)
Extracted molecule genomic DNA
Extraction protocol DNA was purified by phenol/chloroform extraction and ethanol precipitation. Bisulfite conversion was performed using the EZ DNA methylation Kit (Zymo Research). All samples passed bisulfite conversion quality control and were subsequently processed for the Illumina Infinium DNA methylation platform (Human Methylation 450 Bead Chip).
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation HM450 Beadchip using standard Illumina protocol
Scan protocol Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
Description Freshly prepared nuclei (2x10^5 cells) were resuspended in 1X M.SssI reaction buffer (NEB), then treated with 50U of M.SssI (NEB) in 15µL 10X reaction buffer, 45µL 1M sucrose and 0.75µL SAM in a volume of 150uL. Reactions were quenched by the addition of an equal volume of Stop Solution (20nM Tris-HCl [pH 7.9], 600mM NaCl, 1% SDS, 10mM EDTA, 400µg/ml Proteinase K) and incubated at 55°C overnight (Gal-Yam et al., 2006).
Data processing BeadStudio software v3.2
 
Submission date Nov 17, 2014
Last update date Dec 31, 2015
Contact name Xiaojing Yang
E-mail(s) xiaojiny@usc.edu
Phone (323)865-0740
Organization name USC/Norris Comprehensive Cancer Center
Street address 1441 Eastlake Ave, Room 7336
City Los Angeles
State/province CA
ZIP/Postal code 90033
Country USA
 
Platform ID GPL13534
Series (1)
GSE63366 The dynamics of chromatin accessibility during EMT

Data table header descriptions
ID_REF
VALUE normalized Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.38066907 0
cg00000108 0.970366659 0
cg00000109 0.952112637 0
cg00000165 0.370144407 0
cg00000236 0.930094448 0
cg00000289 0.745743043 0
cg00000292 0.928398293 0
cg00000321 0.376161241 0
cg00000363 0.385103544 0
cg00000622 0.323964181 0
cg00000658 0.803207692 0
cg00000714 0.272234029 0
cg00000721 0.942108118 0
cg00000734 0.332567522 0
cg00000769 0.172084563 0
cg00000807 0.712743296 0
cg00000884 0.928405874 0
cg00000905 0.7482022 0
cg00000924 0.53844885 0
cg00000948 0.607333464 0

Total number of rows: 485577

Table truncated, full table size 11813 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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