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Sample GSM263125 Query DataSets for GSM263125
Status Public on Mar 31, 2008
Title MCF7 5-meC
Sample type genomic
 
Channel 1
Source name MCF7
Organism Homo sapiens
Characteristics ChIP sample immunoprecipitated with 5-meC antibody
Extracted molecule genomic DNA
Extraction protocol ChIP assay was performed following the ChIP protocol provided at http://www.genomecenter.ucdavis.edu/farnham and
http://genomecenter.ucdavis.edu/expression_analysis, but instead of heat-denaturation of DNA samples NaOH was added to the IP dilution buffer to the final concentration of 7mM to separate DNA strands.
Label Cy5
Label protocol DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.
 
Channel 2
Source name MCF7
Organism Homo sapiens
Characteristics Total input DNA (control)
Extracted molecule genomic DNA
Extraction protocol ChIP assay was performed following the ChIP protocol provided at http://www.genomecenter.ucdavis.edu/farnham and
http://genomecenter.ucdavis.edu/expression_analysis.
Label Cy3
Label protocol DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.
 
 
Hybridization protocol 12 ug of the Cy5-labeled ChIP sample and 12 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.
Scan protocol Scan Protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)
Description No additional description
Data processing Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel
 
Submission date Feb 06, 2008
Last update date Mar 12, 2008
Contact name Vitalina Komashko
E-mail(s) vitalina.komashko@sagebase.org
Organization name Sage Bionetworks
Street address 1100 Fairview Ave N
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL3787
Series (1)
GSE10504 Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

Data table header descriptions
ID_REF
Rval raw value for Cy5 (from pair file)
Gval raw value for Cy3 (from pair file)
VALUE log2(Rval/Gval) - biweight mean

Data table
ID_REF Rval Gval VALUE
HSAP0406S00000003_CHR1P000008427 9854.11 26883.78 -0.36
HSAP0406S00000003_CHR1P000008667 26600.78 20112.45 1.49
HSAP0406S00000003_CHR1P000008677 26112.78 17568.67 1.66
HSAP0406S00000003_CHR1P000008687 36523.78 22130.55 1.81
HSAP0406S00000003_CHR1P000008697 35847.22 21713.22 1.81
HSAP0406S00000003_CHR1P000008707 31851.45 16753.78 2.02
HSAP0406S00000003_CHR1P000009087 7610.00 7220.00 1.17
HSAP0406S00000003_CHR1P000009097 8711.78 4640.33 2.00
HSAP0406S00000003_CHR1P000009437 15504.22 8605.00 1.94
HSAP0406S00000003_CHR1P000009597 18009.22 19116.89 1.00
HSAP0406S00000003_CHR1P000009607 14556.33 14436.11 1.10
HSAP0406S00000003_CHR1P000009617 9878.44 8623.00 1.29
HSAP0406S00000003_CHR1P000009627 20165.22 19244.22 1.16
HSAP0406S00000003_CHR1P000009637 14675.00 12559.67 1.31
HSAP0406S00000003_CHR1P000009757 5584.44 8529.22 0.48
HSAP0406S00000005_CHR1P000019141 4956.56 4757.44 1.15
HSAP0406S00000005_CHR1P000019171 1983.00 2509.00 0.75
HSAP0406S00000005_CHR1P000019211 1556.44 3183.00 0.06
HSAP0406S00000005_CHR1P000019241 890.44 1901.44 -0.01
HSAP0406S00000005_CHR1P000019251 1030.78 1629.44 0.43

Total number of rows: 359384

Table truncated, full table size 19106 Kbytes.




Supplementary file Size Download File type/resource
GSM263125.pair.gz 6.7 Mb (ftp)(http) PAIR
GSM263125_1.pair.gz 6.8 Mb (ftp)(http) PAIR
Processed data included within Sample table

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