SRX1065227 Pooled Expressors (S288c:?1278b tetrads) gDNA-seq SRP059635 Tetrads sporulated from the cross of Saccharomyces cerevisiae strains ∑1278b and S288c (7 total tetrads, 28 total segregants), selected based on expression of AQY2/ncFRE6, equal amounts of gDNA isolated from each tetrad (n=14), pooled together and whole genome sequenced on the Illumina HiSeq 2500. SRS965124 Whole Genome Sequencing WGS GENOMIC RANDOM 51 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065228 Pooled Non-Expressors (S288c:?1278b tetrads) gDNA-seq SRP059635 Tetrads sporulated from the cross of Saccharomyces cerevisiae strains ∑1278b and S288c (7 total tetrads, 28 total segregants), selected based on expression of AQY2/ncFRE6, equal amounts of gDNA isolated from each tetrad (n=14), pooled together and whole genome sequenced on the Illumina HiSeq 2500. SRS965125 Whole Genome Sequencing WGS GENOMIC RANDOM 51 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065229 S288c_wt_rep1 RNA-seq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain S288c (BY4742) during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965126 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065231 S288c_wt_rep2 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain S288c (BY4742) during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965127 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065235 S288c_(?rim101)_rep1 RNAseq SRP059635 mRNA isolated from Saccharomyces cerevisiae strain S288c (BY4742), with the gene RIM101 removed and replaced by the ∑1278b allele of RIM101, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965130 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065244 S288c_(Sigma-rim101)_rep2 RNAseq SRP059635 mRNA isolated from Saccharomyces cerevisiae strain S288c (BY4742), with the gene RIM101 removed and replaced by the ∑1278b allele of RIM101, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965134 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065245 S288c_rim101?_rep1 RNAseq SRP059635 mRNA isolated from Saccharomyces cerevisiae strain S288c (BY4742), with the gene RIM101 deleted, during mid-log phase after growth in YPD. RNA isolation, poly-A selection followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965140 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065246 S288c_rim101deleted_rep2 RNAseq SRP059635 mRNA isolated from Saccharomyces cerevisiae strain S288c (BY4742), with the gene RIM101 deleted, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965141 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065247 Sigma_wt_rep1 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965142 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065248 Sigma_wt_rep2 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965143 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065249 Sigma_(S288c-rim101)_rep1 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) with the gene RIM101 removed and replaced by the S288c allele of RIM101, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965144 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065251 Sigma_(S288c-rim101)_rep2 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) with the gene RIM101 removed and replaced by the S288c allele of RIM101, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965146 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065252 Sigma_rim101deleted_rep1 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) with the gene RIM101 deleted, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965148 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1065255 Sigma_rim101deleted_rep2 RNAseq SRP059635 mRNA isolated from wild-type Saccharomyces cerevisiae strain Sigma1278b (L6441) with the gene RIM101 deleted, during mid-log phase after growth in YPD. RNA isolation, poly-A selection, followed by reverse transcription to cDNA, and then library preparation using the NEBNext ultra-directional RNA-seq kit. SRS965150 NEBNext Ultra-directional RNAseq RNA-Seq TRANSCRIPTOMIC cDNA 126 0 Application Read Forward 1 Illumina HiSeq 2500 SRX1301575 S288c Reb1 ChIP SRP059635 Briefly, yeast strains were grown to mid-log phase in YPD at 30oC and fixed with 1% formaldehyde for 30 minutes and quenched with glycine for 10 minutes. Cells were pelleted, washed 1X with 10mL 1X TBS, and snap frozen. Cells were lysed in lysis buffer containing 50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, .1% sodium deoxycholate, and protease inhibitors by bead beating 5X for 4 minutes at 4oC. Lysate was transferred to a 15mL conicle, centrifuged at 8500 rpm, and the pellet was washed 2X with lysis buffer. Chromatin was sheared using a Diagenode Bioruptor and immunuprecipitation was performed using anti-myc antibody conjugated to protein G beads overnight at 4oC. Beads were washed 2X with lysis buffer, 2X with lysis buffer + 500mM NaCl, and 2X with wash buffer containing 10mM Tris-HCl pH 8.0, 250mM LiCl, .5% NP40, .5% sodium deoxycholate, and 1mM EDTA. Chromatin was eluted from beads in TE + 1% SDS for one hour at 65oC and cross-links were reversed in TE + .5% SDS for 8 hours at 65oC. DNA was purified using a QIagen PCR Purification kit before proceeding to qPCR or library prep. qPCR was performed using primers specified in supplemental materials and methods. Sequencing libraries were prepared by blunting the sheared DNA, A-tailing, and ligating Illumina Tru-seq adapters. Libraries were size selected and purified using a 2% agarose gel and a Qiagen Gel extraction kit. Adapter-ligated libraries were PCR amplified for 18 cycles and run on the Illumina Hi-seq 2000. SRS1097810 SAMN04128463 Illumina Tru-seq ChIP-Seq GENOMIC ChIP 50 0 Application Read Forward 1 Illumina HiSeq 1500 SRX1301576 Sigma Reb1 ChIP SRP059635 Briefly, yeast strains were grown to mid-log phase in YPD at 30oC and fixed with 1% formaldehyde for 30 minutes and quenched with glycine for 10 minutes. Cells were pelleted, washed 1X with 10mL 1X TBS, and snap frozen. Cells were lysed in lysis buffer containing 50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, .1% sodium deoxycholate, and protease inhibitors by bead beating 5X for 4 minutes at 4oC. Lysate was transferred to a 15mL conicle, centrifuged at 8500 rpm, and the pellet was washed 2X with lysis buffer. Chromatin was sheared using a Diagenode Bioruptor and immunuprecipitation was performed using anti-myc antibody conjugated to protein G beads overnight at 4oC. Beads were washed 2X with lysis buffer, 2X with lysis buffer + 500mM NaCl, and 2X with wash buffer containing 10mM Tris-HCl pH 8.0, 250mM LiCl, .5% NP40, .5% sodium deoxycholate, and 1mM EDTA. Chromatin was eluted from beads in TE + 1% SDS for one hour at 65oC and cross-links were reversed in TE + .5% SDS for 8 hours at 65oC. DNA was purified using a QIagen PCR Purification kit before proceeding to qPCR or library prep. qPCR was performed using primers specified in supplemental materials and methods. Sequencing libraries were prepared by blunting the sheared DNA, A-tailing, and ligating Illumina Tru-seq adapters. Libraries were size selected and purified using a 2% agarose gel and a Qiagen Gel extraction kit. Adapter-ligated libraries were PCR amplified for 18 cycles and run on the Illumina Hi-seq 2000. SRS1097811 SAMN04128464 Illumina Tru-seq ChIP-Seq GENOMIC ChIP 50 0 Application Read Forward 1 Illumina HiSeq 2000