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Sample GSM262742 Query DataSets for GSM262742
Status Public on Mar 31, 2008
Title mESc E14 5-meC
Sample type genomic
 
Channel 1
Source name mESc E14
Organism Mus musculus
Characteristics ChIP sample immunoprecipitated with 5-meC antibody
Extracted molecule genomic DNA
Extraction protocol Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. ChIP assay with 5-Methylcytidine antibody was performed using ChIP-IT Express kit (Active Motif, cat#53008)
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 Cells were lysed by shaking at 50C o/n in digestion buffer (100mM NaCl; 10mM Tris Cl, pH 8; 25mM EDTA, pH 8; 0.5% SDS; 0.1 mg/ml proteinase K) and genomic DNA was extracted with phenol-chloroform/isoamyl alcohol. DNA was sonicated.
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 1995.89 2256.33 -0.13
MMUS0407S00000001_CHR1P004094180 7425.33 5987.44 0.36
MMUS0407S00000001_CHR1P004094190 10874.00 8641.33 0.38
MMUS0407S00000001_CHR1P004094200 11725.11 10420.33 0.22
MMUS0407S00000001_CHR1P004094210 9643.22 9852.56 0.02
MMUS0407S00000001_CHR1P004094240 3086.33 3407.22 -0.09
MMUS0407S00000001_CHR1P004094270 3065.11 2879.44 0.14
MMUS0407S00000001_CHR1P004094280 2596.56 2436.22 0.14
MMUS0407S00000001_CHR1P004094290 2897.44 2227.11 0.43
MMUS0407S00000001_CHR1P004094310 9612.22 9132.11 0.12
MMUS0407S00000001_CHR1P004094320 5509.44 5699.22 0.00
MMUS0407S00000001_CHR1P004094330 6847.44 6014.11 0.24
MMUS0407S00000001_CHR1P004094340 12960.89 12959.56 0.05
MMUS0407S00000001_CHR1P004094380 4292.22 4472.44 -0.01
MMUS0407S00000001_CHR1P004094410 1238.67 763.33 0.75
MMUS0407S00000002_CHR1P004094157 1780.44 1422.78 0.37
MMUS0407S00000002_CHR1P004094177 6702.44 4945.00 0.49
MMUS0407S00000002_CHR1P004094187 8716.11 6777.56 0.41
MMUS0407S00000002_CHR1P004094197 11254.89 9685.44 0.27
MMUS0407S00000002_CHR1P004094207 11276.67 11929.00 -0.03

Total number of rows: 386424

Table truncated, full table size 20792 Kbytes.




Supplementary file Size Download File type/resource
GSM262742.pair.gz 6.5 Mb (ftp)(http) PAIR
GSM262742_1.pair.gz 6.5 Mb (ftp)(http) PAIR
Processed data included within Sample table

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