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Sample GSM955410 Query DataSets for GSM955410
Status Public on Jul 11, 2012
Title H3K4me3 vs Input at t=30
Sample type genomic
 
Channel 1
Source name yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: By4741
sample type: Input
time: 30 minutes
Growth protocol Yeast cells By4741 were grown to mid-log on YPD and At “time zero” cells were treated with 1.5mM diamide (D3648, Sigma).
Extracted molecule genomic DNA
Extraction protocol At t = 0, 4, 8, 15, 30, and 60 minutes, cells were fixed by 1% formaldehyde, followed after 15 minutes by quenching with 125 mM glycine. Cells were then pelleted, washed with water, and subjected to MNase digestion as previously described (Kaplan et al., Plos Genetics 2008; Radman-Livaja et al., PLoS Genetics, 2010) and immunoprecipitation.
Label Cy5
Label protocol ChIP material was amplified using the DNA linear amplification method described previously (Liu et al., 2005; Liu et al., 2003). 3ug of the amplified ChIP products was labeled via the amino-allyl methods as described on http://www.microarrays.org.
 
Channel 2
Source name yeast cells
Organism Saccharomyces cerevisiae
Characteristics strain: By4741
antibody: anti-H3K4me3
vendor/catalog/lot: Millipore 04-745 NG1643014
time: 30 minutes
Growth protocol Yeast cells By4741 were grown to mid-log on YPD and At “time zero” cells were treated with 1.5mM diamide (D3648, Sigma).
Extracted molecule genomic DNA
Extraction protocol At t = 0, 4, 8, 15, 30, and 60 minutes, cells were fixed by 1% formaldehyde, followed after 15 minutes by quenching with 125 mM glycine. Cells were then pelleted, washed with water, and subjected to MNase digestion as previously described (Kaplan et al., Plos Genetics 2008; Radman-Livaja et al., PLoS Genetics, 2010) and immunoprecipitation.
Label Cy3
Label protocol ChIP material was amplified using the DNA linear amplification method described previously (Liu et al., 2005; Liu et al., 2003). 3ug of the amplified ChIP products was labeled via the amino-allyl methods as described on http://www.microarrays.org.
 
 
Hybridization protocol Labeled probes (a mixture of Cy5-labeled input and Cy3-labeled ChIP-ed material) were hybridized onto an Agilent yeast tiled oligonucleotide microarray (G4495A) at 65°C for 16 h and washed as described on http://www.microarrays.org
Scan protocol The arrays were scanned at 5 μ resolution with an Agilent scanner.
Images were quantified using Agilent Feature Extraction Software.
Description MNase-ChIP vs input
Data processing Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.
 
Submission date Jul 03, 2012
Last update date Jul 11, 2012
Contact name Nir Friedman
E-mail(s) [email protected]
Organization name Hebrew University
Street address Givat Ram
City Jerusalem
ZIP/Postal code 91904
Country Israel
 
Platform ID GPL10930
Series (1)
GSE39080 Systematic dissection of roles for chromatin regulators in a yeast stress response

Data table header descriptions
ID_REF
VALUE normalized log10 ratio test/reference
INV_VALUE normalized log10 ratio (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
A_75_P01227278 0.317 -3.17E-01
A_75_P02174712 -0.365 3.65E-01
A_75_P01356122 -0.0641 6.41E-02
A_75_P01360957 0.424 -4.24E-01
A_75_P01528814 -0.199 1.99E-01
A_75_P01502655 0.0507 -5.07E-02
A_75_P01024026 -0.298 2.98E-01
A_75_P01431089 -0.557 5.57E-01
A_75_P02016198 0.399 -3.99E-01
A_75_P01805398 -0.0999 9.99E-02
A_75_P01461781 -0.0813 8.13E-02
A_75_P01587413 -0.337 3.37E-01
A_75_P01561270 -0.0502 5.02E-02
A_75_P01501338 0.0778 -7.78E-02
A_75_P01733962 0.127 -1.27E-01
A_75_P02044236 -0.256 2.56E-01
A_75_P01459590 0.618 -6.18E-01
A_75_P01963931 0.141 -1.41E-01
A_75_P01732629 -0.324 3.24E-01
A_75_P01894690 0.531 -5.31E-01

Total number of rows: 41775

Table truncated, full table size 1271 Kbytes.




Supplementary file Size Download File type/resource
GSM955410_US45102941_251481011310_S01_ChIP_107_Sep09_Lowess_BGsub_1_3.txt.gz 13.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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