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Sample GSM1323585 Query DataSets for GSM1323585
Status Public on Dec 31, 2014
Title H3K27me3 of CpG island in MCF7
Sample type genomic
 
Channel 1
Source name Sonicated MCF7 chromatin (WCE)
Organism Homo sapiens
Characteristics cell line: MCF7
cell fraction: WCE
Growth protocol Du145, PC3, MCF7, MDA-MB-231, and RKO were maintained in RPMI1640 medium. HCT116 was maintained in McCoy's 5A medium. RWPE1 was maintained in keratinocyte-SFM. HMEC was maintained in mammary epithelial cell serum-free growth medium. FHC was maintained in mixture of Ham's F12 and DMEM (1:1).
Extracted molecule genomic DNA
Extraction protocol About 1 x 10e7 cells were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).
Label Cy3
Label protocol Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K27me3 (07-449, Millipore) at 4ºC overnight. Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl. After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 30 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).
 
Channel 2
Source name Sonicated MCF7 chromatin (IP)
Organism Homo sapiens
Characteristics cell line: MCF7
cell fraction: IP
antibody: H3K27me3
Growth protocol Du145, PC3, MCF7, MDA-MB-231, and RKO were maintained in RPMI1640 medium. HCT116 was maintained in McCoy's 5A medium. RWPE1 was maintained in keratinocyte-SFM. HMEC was maintained in mammary epithelial cell serum-free growth medium. FHC was maintained in mixture of Ham's F12 and DMEM (1:1).
Extracted molecule genomic DNA
Extraction protocol About 1 x 10e7 cells were cross-linked with 1 % formaldehyde, lysed, and sonicated with a Bioruptor UCD-250 (Cosmo Bio, Tokyo, Japan).
Label Cy5
Label protocol Solubilized chromatin was diluted 10-fold in dilution buffer [50 mM Tris-HCl, pH 8.0, 167 mM NaCl, 1.1 % (w/v) Triton X-100, 0.11 % (w/v) sodium deoxycholate (DOC)], and incubated with antibody against H3K27me3 (07-449, Millipore) at 4ºC overnight. Immuno-complexes were collected with Dynabeads Protein A, washed with 1 x RIPA buffer [50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, 1 % (w/v) Triton X-100, 0.1 % (w/v) SDS, 0.1 % (w/v) DOC] containing 150 mM NaCl, 1 x RIPA buffer containing 500 mM NaCl, LiCl wash buffer [10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 1 mM EDTA, 0.5 % (w/v) NP-40, 0.5 % (w/v) DOC] and 1 x TE containing 50 mM NaCl. After cross-link reversal, DNA was recovered with RNaseA and proteinase K treatment, followed by phenol extraction and ethanol precipitation, and dissolved in 30 μl of 1 x TE. 500 ng of DNA was labeled using Agilent Genomic DNA labeling Kit PLUS (5188-5309).
 
 
Hybridization protocol Labelled DNA mixed with cot-1 DNA and Agilent blocking solution was hybridized to microarray for 40 hours at 67℃ and 20 rpm rotation. Microarrays was washed according to Agilent protocol.
Scan protocol The microarray was scanned with an Agilent G2565BA microarray scanner (Agilent Technologies).
Description Untreated cells
Data processing Scanned data was analyzed with Feature Extraction Ver.9.1 and normalized (Background subtraction) using Agilent G4477AA ChIP Analytics 1.3 software.
 
Submission date Feb 06, 2014
Last update date Dec 31, 2014
Contact name Hideyuki Takeshima
E-mail(s) takeshima.hideyuki@hoshi.ac.jp
Organization name Hoshi University
Department Institute for Advanced Life Sciences
Lab Department of Epigenomics
Street address 2-4-41 Ebara
City Shinagawa-ku
State/province Tokyo
ZIP/Postal code 142-8501
Country Japan
 
Platform ID GPL9767
Series (1)
GSE54758 DNA methylation, H3K27me3, and gene expression statuses of human cancer cell lines and normal cells.

Data table header descriptions
ID_REF
VALUE Normalized log2 (IP/WCE) ratio

Data table
ID_REF VALUE
A_17_P00000030 0.169925
A_17_P00000058 0.3971474
A_17_P00000077 0.7651993
A_17_P00000078 1.2148192
A_17_P00000079 2.2947738
A_17_P00000131 0.21089678
A_17_P00000132 1.6793119
A_17_P00000133 0.52124876
A_17_P00000171 0.9670496
A_17_P00000172 0.91378206
A_17_P00000173 0.5206477
A_17_P00000174 -0.037967864
A_17_P00000175 0.30072078
A_17_P00000176 -0.39980292
A_17_P00000177 1.3307953
A_17_P00000239 0.14185269
A_17_P00000240 1.860819
A_17_P00000241 0.725825
A_17_P00000242 1.6312402
A_17_P00000243 1.5881249

Total number of rows: 237202

Table truncated, full table size 5834 Kbytes.




Supplementary file Size Download File type/resource
GSM1323585_MCF7_H3K27me3_251479116506.txt.gz 25.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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