Comment[ArrayExpressAccession]	E-GEOD-67912
MAGE-TAB Version	1.1		
Public Release Date	2015-08-21
Investigation Title	Bas1 and Ino4 ChIP-seq		
Comment[Submitted Name]	Bas1 and Ino4 ChIP-seq
Experiment Description	Meiotic recombination is initiated by developmentally programmed DNA double-strand breaks (DSBs). In S. cerevisiae, the vast majority of DSBs occur in the nucleosome-depleted regions at gene promoters, where transcription factors (TFs) bind. It has been proposed that TF binding can stimulate DSB formation nearby by modulating local chromatin structure. However, a prior study in TF bas1 mutant suggested that the role of TF binding in determining break formation is complex. Here, we examined fine-scale DSB distributions in TF mutant (bas1Δ and ino4Δ) strains. In bas1Δ mutants, 239 out of the 2468 hotspots showed reduced DSB activity, whereas 87 hotspots showed increased DSB activity. Similarly, in ino4Δ mutant, 415 out of the 2468 hotspots showed reduced DSB activity, whereas 322 hotspots showed increased DSB activity. We also mapped Bas1 and Ino4 binding sites in meiosis and found that only a small portion of the affected hotspots contained TF binding sites. This indicates that TF can influence DSB distribution both directly and indirectly. Surprisingly, these DSB changes in TF mutants did not correlate with change in chromatin structure and histone H3K4me3 modification, suggesting that the role of TF on DSB distribution cannot be simply explained by affecting local chromatin status. Four samples total: Bas1-Myc (ChIP and input samples), Ino4-Myc (ChIP and input samples)		
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	Zhao	Zhu	Keeney
Person First Name	Jeffrey	Xuan	Scott
Person Email	zhaoy@mskcc.org		
Person Affiliation	Memorial Sloan Kettering Cancer Center		
Person Address	Genomics Core, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, USA		
Person Roles	submitter		
Protocol Name	P-GSE67912-3	P-GSE67912-2	P-GSE67912-1
Protocol Description	Reads were mapped to the S. cerevisiae sacCer2 genome assembly using BWA mem (version 0.7.5a-r405) to generate coverage maps for each data set. Genome_build: The SGD assembly released in June 2008, called sacCer2 by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645 Supplementary_files_format_and_content: Text files of coverage maps	ChIP was performed as described (Murakami et al., 2014). Cells were sporulated and 50 mL of meiotic culture (2 x 109 cells) was collected at 4h and crosslinked with 1% formaldehyde for 30 min at room temperature. Crosslinking was terminated by 5 min incubation with 131 mM glycine. Cells were washed twice with ice-cold TBS, flash frozen with liquid nitrogen and stored at -80°C. Cells were suspended in 1 mL of Lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 1 mM PMSF, 7 ug/mL aprotinin, 1% protease inhibitor cocktail (Sigma), 1x Complete Protease Inhibitor Cocktail (Roche)) with ca. 900 uL of 0.5 mm zirconia/silica beads (BioSpec Products) in 2 mL screw-cap tubes. Cells were disrupted by vigorous shaking 3 min x 6 times in Mini-beadbeater-16 (BioSpec Products) or at 6.5 m/s for 1 min x 8 times in FastPrep24 (MP Biomedicals). 1 mL of Lysis buffer was added after cell disruption. Subsequently, chromatin in the whole cell extracts (WCE) was sheared by sonication with "M" intensity, 30 sec ON/ 30 sec OFF for 15 min x 2 times in Bioruptor Sonication System UCD200 (Diagenode) in 15 mL polystyrene conical tubes. Insoluble fraction (cell debris) was removed by centrifugation at 21,130 g, 5 min, 4°C. WCE was further sonicated with the same conditions 1-3 times to yield average DNA size less than 500 bp. WCE was flash frozen and stored at -80°C. The ChIPseq library was prepared following Illumina standard protocol. We used Trueseq DNA sample prep kit.	Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 13.5–14 hr at 30ºC, harvested, resuspended in 2% potassium acetate, and sporulated at 30ºC.
Protocol Type	normalization data transformation protocol	nucleic acid library construction protocol	growth protocol
Experimental Factor Name	epitope tag		
Experimental Factor Type	epitope tag		
Publication Title	High-Resolution Global Analysis of the Influences of Bas1 and Ino4 Transcription Factors on Meiotic DNA Break Distributions in Saccharomyces cerevisiae.		
Publication Author List	Zhu X, Keeney S		
PubMed ID	26245832		
Publication DOI	10.1534/genetics.115.178293		
Comment[SecondaryAccession]	GSE67912		
Comment[GEOReleaseDate]	2015-08-21		
Comment[ArrayExpressSubmissionDate]	2015-04-15		
Comment[GEOLastUpdateDate]	2015-08-21		
Comment[AEExperimentType]	ChIP-seq		
Comment[SecondaryAccession]	SRP057262		
Comment[SequenceDataURI]	http://www.ebi.ac.uk/ena/data/view/SRR1976518-SRR1976521		
SDRF File	E-GEOD-67912.sdrf.txt