Comment[ArrayExpressAccession]	E-GEOD-43001
MAGE-TAB Version	1.1						
Public Release Date	2013-07-24
Investigation Title	The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)						
Comment[Submitted Name]	The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress (rapamycin or DMSO)
Experiment Description	Snt2 is a yeast chromatin-interacting protein whose function has not been well characterized, that was recently shown to associate with Ecm5 and the Rpd3 deacetylase. Using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), we show that in response to H2O2, Snt2 and Ecm5 colocalize to promoters of genes involved in various aspects of the environmental stress response. By integrating these ChIP-seq results with expression analysis, we identify a key set of target genes that require Snt2 for proper expression after H2O2 stress. Finally, by mapping Snt2 and Ecm5 localization before and after rapamycin treatment, we identify a subset of H2O2-specific Snt2 and Ecm5 target promoters that are also targeted in response to rapamycin. Our results establish a function for Snt2 in regulating transcriptional changes in response to oxidative stress, and suggest Snt2 may have a role in additional stress pathways. Crosslinking ChIP analysis to identify sites of Snt2 or Ecm5 genomic localization before, 0.5 hours after, or 4 hours after treatment with rapamycin (final concentration 5 nM) or with DMSO as a control. Snt2 and Ecm5 were genomically tagged with a 13Myc tag at their C termini. ChIPs were performed using a Myc antibody on either Snt2-Myc or Ecm5-Myc strains, or on untagged wildtype strain (BY4741) as a control. Inputs and ChIPs from untagged strain were sequenced as controls.						
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl					
Person Last Name	Allis	Baker	Dewell	Zheng	Allis	Ueberheide	Chait
Person First Name	David	Lindsey	Scott	Deyou	C	Beatrix	Brian
Person Mid Initials		A			D	M	T
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	The Rockefeller University						
Person Address	Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Ave Box 78, New York, NY, USA						
Person Roles	submitter						
Protocol Name	P-GSE43001-4	P-GSE43001-1	P-GSE43001-3	P-GSE43001-2			
Protocol Description	ChIP-seq reads were aligned at 51bp to the SacCer2 genome assembly using Bowtie: only unique reads with no more than 2 mismatches were kept Aligned BAM files were converted to Wig files using IGVtools Genome_build: sacCer2	An aliquot of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. Each culture was then divided into two separate cultures: one of these was treated with rapamycin dissolved in DMSO (final rapamycin concentration 50 nM), while the other cultures was treated with DMSO as a control. Samples were taken 0.5 and 4 hours after treatment for ChIP/Inputs.	Samples were crosslinked by adding formaldehyde (final conc 1%) at room temp for 20 minutes, and then quenched with glycine (final conc 125 mM). ChIPs were performed as described (Aparicio et al. 2005 Curr Protoc Mol Biol). Briefly cells were lysed using glass beads, and chromatin was sheared to 150-500 bp. Chromatin was isolated and used for ChIP with the anti-Myc 9E10 antibody (Millipore #05-419) according to standard procedures. Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Sample Preparation Kit (cat # FC-121-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 21 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.	Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.4)			
Protocol Type	normalization data transformation protocol	sample treatment protocol	nucleic acid library construction protocol	growth protocol			
Experimental Factor Name	HOURS TREATMENT	TREATMENT	YEAST STRAIN	ANTIBODY			
Experimental Factor Type	hours treatment	treatment	yeast strain	antibody			
Comment[SecondaryAccession]	GSE43001						
Comment[GEOReleaseDate]	2013-07-24						
Comment[ArrayExpressSubmissionDate]	2012-12-18						
Comment[GEOLastUpdateDate]	2013-07-28						
Comment[AEExperimentType]	ChIP-seq						
Comment[SecondaryAccession]	SRP017605						
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR636665-SRR636694						
SDRF File	E-GEOD-43001.sdrf.txt