ERX4489751 E-MTAB-9499:Chassis_F 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040725 SAMEA7280124 Chassis_F 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain Chassis_F ERX4489752 E-MTAB-9499:Chassis_F 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040726 SAMEA7280125 Chassis_F 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain Chassis_F ERX4489753 E-MTAB-9499:Chassis_F 3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040727 SAMEA7280126 Chassis_F 3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain Chassis_F ERX4489754 E-MTAB-9499:Chassis_Mz 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040728 SAMEA7280127 Chassis_Mz 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain Chassis_Mz ERX4489755 E-MTAB-9499:Chassis_Mz 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040729 SAMEA7280128 Chassis_Mz 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain Chassis_Mz ERX4489756 E-MTAB-9499:Chassis_Mz 3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040730 SAMEA7280129 Chassis_Mz 3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain Chassis_Mz ERX4489757 E-MTAB-9499:Chassis_Sz 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040731 SAMEA7280130 Chassis_Sz 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 sdh3 zwf1 Experimental Factor: strain Chassis_Sz ERX4489758 E-MTAB-9499:Chassis_Sz 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040732 SAMEA7280131 Chassis_Sz 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 sdh3 zwf1 Experimental Factor: strain Chassis_Sz ERX4489759 E-MTAB-9499:E_Chassis_F 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040733 SAMEA7280132 E_Chassis_F 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain E_Chassis_F ERX4489760 E-MTAB-9499:E_Chassis_F 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040734 SAMEA7280133 E_Chassis_F 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain E_Cassis_F ERX4489761 E-MTAB-9499:E_Chassis_F 3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040735 SAMEA7280134 E_Chassis_F 3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 ser3 ser33 fum1 Experimental Factor: strain E_Chassis_F ERX4489762 E-MTAB-9499:E_Chassis_Mz 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040736 SAMEA7280135 E_Chassis_Mz 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain E_Chassis_Mz ERX4489763 E-MTAB-9499:E_Chassis_Mz 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040737 SAMEA7280136 E_Chassis_Mz 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain E_Chassis_Mz ERX4489764 E-MTAB-9499:E_Chassis_Mz 3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040738 SAMEA7280137 E_Chassis_Mz 3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 zwf1 mdh1 mdh2 mae1 Experimental Factor: strain E_Chassis_Mz ERX4489765 E-MTAB-9499:E_Chassis_Sz 1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040739 SAMEA7280138 E_Chassis_Sz 1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 sdh3 zwf1 Experimental Factor: strain E_Chassis_Sz ERX4489766 E-MTAB-9499:E_Chassis_Sz 2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040740 SAMEA7280139 E_Chassis_Sz 2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 sdh3 zwf1 Experimental Factor: strain E_Chassis_Sz ERX4489767 E-MTAB-9499:E_Chassis_Sz 3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040741 SAMEA7280140 E_Chassis_Sz 3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MAT URA3 HIS3 LEU2 TRP1 MAL2- 8c SUC2 ser3 ser33 sdh3 zwf1 Experimental Factor: strain E_Chassis_Sz ERX4489768 E-MTAB-9499:WT_1_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040742 SAMEA7280141 WT_1_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MATa URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 Experimental Factor: strain CEN.PK113-7D ERX4489769 E-MTAB-9499:WT_2_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040743 SAMEA7280142 WT_2_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MATa URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 Experimental Factor: strain CEN.PK113-7D ERX4489770 E-MTAB-9499:WT_3_s ERP123698 PRJEB40099 RNA-seq analysis of model-guided engineered Saccharomyces cerevisiae chassis for improved dicarboxylic acids (malic, succinic and fumaric acid) production. ERS5040744 SAMEA7280143 WT_3_s RNA-Seq TRANSCRIPTOMIC PolyA Samples were collected at mid-exponential growth phase for transcriptomics, proteomics and extracellular metabolomics. For total RNA, 10 mL of culture broth was collected in a 50 mL Falcon® tube filled with ice and immediately centrifuged at 10.000rpm for 2 min at 0 °C. After centrifugation, cell pellet were snap-frozen in liquid nitrogen and kept at -80°C until extraction. Pre-cultures were prepared by cultivating a single colony from a selective YPD plate of each yeast strain in YPD medium until mid-exponential phase (~16 h). Pre-cultured cells were centrifuged, washed two times with distilled water, and inoculated in defined minimal media with 2% glucose at initial OD600 of 0.1. These cultivations were performed in triplicates. Total RNA was isolated with RNAeasy kit (Qiagen) following manufacturer recommendations. To remove DNA contamination, samples were digested with Turbo DNAse (Invitrogen Ambion) followed by RNA clean-up (RNAeasy kit, Qiagen). RNA library was prepared using the NEBNext® Ultra™ II Directional RNA Library Preparation Kit for Illumina: polyA transcripts capture. Barcoded stranded mRNA-seq libraries were prepared from ~200 ng total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA). NextSeq 500 Experimental Factor: genotype MATa URA3 HIS3 LEU2 TRP1 MAL2-8c SUC2 Experimental Factor: strain CEN.PK113-7D