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Sample GSM462289 Query DataSets for GSM462289
Status Public on Nov 12, 2009
Title Primary_human_keratinocytes_MeDIP_+Ca_1of2
Sample type genomic
 
Channel 1
Source name Primary Human Keratinocytes; Differentiation conditions; MeDIP profiling
Organism Homo sapiens
Characteristics cell type: primary keratinocytes
gender: male
tissue: foreskin
status: differentiated
antibody: monoclonal anti-5-methylcytidine antibody
Treatment protocol Methylated DNA was immunopreciptated from primary human keratinoctyes cultured in high calcium differentiation conditions.
Growth protocol Keratinocytes were cultured in Gibco SFM until confluent at which point 1.2mM Ca was added for 3 days to induce differentiation.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from cells using the DNeasy kit (Qiagen). The DNA was sonicated to produce fragments from 300 to 1,000 bp and subject to immunoprecipitation using a monoclonal antibody against 5-methylcytidine (Eurogentec) according to published protocols (Weber, M. et al., 2007, Nat. Genet.) DNA enriched for 5-methylcytidine was subject to amplification using the Whole Genome Amplification kit (Sigma) according to manufacturers protocol.
Label Cy5
Label protocol Labeling was performed by NimbleGen.
 
Channel 2
Source name input
Organism Homo sapiens
Characteristics antibody: none
Treatment protocol Methylated DNA was immunopreciptated from primary human keratinoctyes cultured in low calcium growth conditions.
Growth protocol Keratinocytes were cultured in Gibco SFM in subconfluent conditions.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from cells using the DNeasy kit (Qiagen). The DNA was sonicated to produce fragments from 300 to 1,000 bp and subject to immunoprecipitation using a monoclonal antibody against 5-methylcytidine (Eurogentec) according to published protocols (Weber, M. et al., 2007, Nat. Genet.) DNA enriched for 5-methylcytidine was subject to amplification using the Whole Genome Amplification kit (Sigma) according to manufacturers protocol.
Label Cy3
Label protocol Labeling was performed by NimbleGen.
 
 
Hybridization protocol Hybridization was performed by NimbleGen.
Scan protocol Scanning was performed by NimbleGen.
Description Human foreskin keratinocytes; Differentiated; methylated DNA immunoprecipitation profiling on promoter tiling arrays.
Data processing Raw .pair files were loaded into NimbleScan to produce subsequent .GFF ratio and peak files. Default parameters were used.
 
Submission date Oct 15, 2009
Last update date Nov 12, 2009
Contact name Paul A Khavari
Organization name Stanford University
Department Dermatology
Lab Khavari Lab
Street address 259 Campus Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5168
Country USA
 
Platform ID GPL6325
Series (1)
GSE18590 DNMT1 Maintains Progenitor Function in Self-Renewing Somatic Tissue

Data table header descriptions
ID_REF
VALUE GFF ratio, log2(MeDIP/input)

Data table
ID_REF VALUE
CHR10P001020948 -0.16
CHR10P001021048 0.09
CHR10P001026162 0.62
CHR10P001022248 -0.2
CHR10P001023448 -0.36
CHR10P001023148 0.43
CHR10P001026962 1.22
CHR10P001021248 -0.15
CHR10P001021748 0.45
CHR10P001024348 0.37
CHR10P001026062 0.47
CHR10P001021648 0.23
CHR10P001023548 -0.43
CHR10P001023248 -0.05
CHR10P001027262 0.85
CHR10P001022548 0.51
CHR10P001025462 0.65
CHR10P001026762 0.75
CHR10P001027562 0.28
CHR10P001021348 -0.39

Total number of rows: 378943

Table truncated, full table size 7910 Kbytes.




Supplementary file Size Download File type/resource
GSM462289_532.pair.gz 6.9 Mb (ftp)(http) PAIR
GSM462289_635.pair.gz 7.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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