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Sample GSM1103385 Query DataSets for GSM1103385
Status Public on Apr 21, 2013
Title H3 turnover in swi6chp2 deletion mutant
Sample type genomic
 
Channel 1
Source name whole cell extract (WCE) genomic DNA
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: swi6chp2 deletion mutant
antibody: None (whole cell extract)
Treatment protocol Cells were crosslinked with 1% Formaldehyde
Growth protocol Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized by Hydroxyurea and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose.
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted from cross-linked cells following lysis with bead beater and using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody. After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by Qiagen QIAquick PCR column.
Label Cy3
Label protocol WCE DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy3 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column
 
Channel 2
Source name swi6chp2 deletion mutant - H3-FLAG IP
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: swi6chp2 deletion mutant
antibody: anti-FLAG
Treatment protocol Cells were crosslinked with 1% Formaldehyde
Growth protocol Exponentially growing cultures of fission yeast cells expressing an ectopic copy of FLAG tagged histone H3 under the control of inv1 promoter were synchronized by Hydroxyurea and expression of H3-FLAG was induced by changing the carbon source of the medium to Sucrose.
Extracted molecule genomic DNA
Extraction protocol Chromatin was extracted from cross-linked cells following lysis with bead beater and using micrococcal nuclease (MNase). Chromatin immunoprecipitated DNA recovered with anti-FLAG antibody. After reverse cross-linked and digested with Rnase A and proteinase K, DNA was recovered by Qiagen QIAquick PCR column.
Label Cy5
Label protocol ChIP DNA after amplified by random priming PCR incorporating amino-allyl dUTP was covalently coupled with Cy5 mono NHS ester in 100 mM sodium bicarbonate for 1 hr at room temperature. Labeled DNA was recovered by Qiagen QIAquick PCR column
 
 
Hybridization protocol 500 ng of Cy3 labeled WCE DNA was mixed with 500 ng of Cy5 labeled ChIP DNA plus 50 ul Agilent 10X control targets and 250 ul of 2X Agilent Hybridization buffer
Scan protocol Slides were scanned using Agilent scanner and image intensity data were extracted and analyzed with Agilent Feature Extraction software version 8.5
Data processing Log ratios of ChIP over WCE were obtained by dividing normalized median Cy5 value over its corrresponding Cy3 value
 
Submission date Mar 21, 2013
Last update date Apr 21, 2013
Contact name Shiv Grewal
Phone 2407607553
Organization name NCI
Department LBMB
Lab Shiv Grewal
Street address NCI bldg 37 Rm 6068 9000 Rockville Pike
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL11244
Series (1)
GSE45378 HDAC mediated suppression of histone turnover promotes epigenetic stability of heterochromatin

Data table header descriptions
ID_REF
VALUE normalized log2 ratios of medians defined as normalized Ch2 (Cy5) divided by Ch1 (Cy3)

Data table
ID_REF VALUE
1 -0.247226152
2 -0.243671233
3 -0.240744647
4 -0.23824978
5 -0.236246654
6 -0.234741881
7 -0.233612697
8 -0.232892098
9 -0.232561956
10 -0.232594414
11 -0.232945976
12 0.444645168
13 0.951120608
14 0.074471496
15 -0.207113
16 0.883917814
17 -0.311952379
18 0.204371422
19 -0.016439548
20 -0.145434934

Total number of rows: 45220

Table truncated, full table size 801 Kbytes.




Supplementary file Size Download File type/resource
GSM1103385_US11213905_251735810025_S01_ChIP-v1_95_May07_1_3.txt.gz 4.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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