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Sample GSM262741 Query DataSets for GSM262741
Status Public on Mar 31, 2008
Title mESc E14 H3me3K9
Sample type genomic
 
Channel 1
Source name mESc E14
Organism Mus musculus
Characteristics ChIP sample immunoprecipitated with H3me3K9 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.
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 mESc E14
Organism Mus musculus
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 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 05, 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 GPL3793
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
MMUS0407S00000001_CHR1P004094150 1542.89 1191.33 0.40
MMUS0407S00000001_CHR1P004094180 3950.11 3898.22 0.05
MMUS0407S00000001_CHR1P004094190 5292.89 4775.33 0.18
MMUS0407S00000001_CHR1P004094200 4373.56 3157.89 0.50
MMUS0407S00000001_CHR1P004094210 5673.78 2796.11 1.05
MMUS0407S00000001_CHR1P004094240 2384.11 1901.11 0.36
MMUS0407S00000001_CHR1P004094270 2052.11 1273.78 0.72
MMUS0407S00000001_CHR1P004094280 2283.56 2536.00 -0.12
MMUS0407S00000001_CHR1P004094290 3478.33 3524.11 0.01
MMUS0407S00000001_CHR1P004094310 2804.00 3942.22 -0.46
MMUS0407S00000001_CHR1P004094320 2990.78 2643.56 0.21
MMUS0407S00000001_CHR1P004094330 4238.22 3406.22 0.35
MMUS0407S00000001_CHR1P004094340 4103.44 4333.33 -0.05
MMUS0407S00000001_CHR1P004094380 1785.89 2107.78 -0.21
MMUS0407S00000001_CHR1P004094410 1790.11 1190.56 0.62
MMUS0407S00000002_CHR1P004094157 2508.11 1436.00 0.84
MMUS0407S00000002_CHR1P004094177 3973.22 4461.78 -0.14
MMUS0407S00000002_CHR1P004094187 4294.67 3204.33 0.45
MMUS0407S00000002_CHR1P004094197 4335.44 3414.22 0.38
MMUS0407S00000002_CHR1P004094207 3619.33 3569.67 0.05

Total number of rows: 386424

Table truncated, full table size 20236 Kbytes.




Supplementary file Size Download File type/resource
GSM262741.pair.gz 6.4 Mb (ftp)(http) PAIR
GSM262741_1.pair.gz 6.4 Mb (ftp)(http) PAIR
Processed data included within Sample table

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