Comment[ArrayExpressAccession]	E-GEOD-43002
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							
Comment[Submitted Name]	The yeast Snt2 protein helps coordinate the transcriptional response to hydrogen-peroxide mediated oxidative stress
Experiment Description	This SuperSeries is composed of the SubSeries listed below. Refer to individual Series							
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							
Person First Name	David							
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-GSE43002-1	P-GSE43002-4	P-GSE43002-7	P-GSE43002-6	P-GSE43002-3	P-GSE43002-8	P-GSE43002-2	P-GSE43002-5
Protocol Description	One third of each yeast culture was taken for the 0 hour (T0) ChIP/Input samples. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 and 4 hours after H2O2 addition for ChIP/Inputs	One half of each yeast culture was taken for the 0 hour (T0) sample. H2O2 was added to remaining cultures at a final concentration of 0.4 mM. Samples were taken 0.5 hours after H2O2 addition for the 0.5 hour (T0.5) sample.	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.	Total RNA was obtained through hot acid phenol extraction (Collart, M. A., and S. Oliviero. 200; Current Prot. Mol. Bio.) Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit (cat # RS-122-2001). After adapter ligation DNA was PCR amplified with Illumina primers for 15 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.	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 20 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. 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.	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)	Saturated overnight cultures of strains (Snt2-Myc, Ecm5-Myc, or BY4741) were diluted in YPD and grown to mid-log phase (OD600=0.3).
Protocol Type	sample treatment protocol	sample treatment protocol	sample treatment protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	nucleic acid library construction protocol	growth protocol	growth protocol
Experimental Factor Name	HOURS TREATMENT	TREATMENT	BIOL. REPLICATE #	HOURS H2O2	YEAST STRAIN	ANTIBODY		
Experimental Factor Type	hours treatment	treatment	biol. replicate #	hours h2o2	yeast strain	antibody		
Comment[SecondaryAccession]	GSE43002							
Comment[GEOReleaseDate]	2013-07-24							
Comment[ArrayExpressSubmissionDate]	2012-12-18							
Comment[GEOLastUpdateDate]	2013-07-24							
Comment[AEExperimentType]	RNA-seq of coding RNA							
Comment[AEExperimentType]	ChIP-seq							
SDRF File	E-GEOD-43002.sdrf.txt