SRX1748448 GSM2144512 SRP074582 SRS1426239 GSM2144512 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144512 GEO Accession GSM2144512 SRX1748449 GSM2144513 SRP074582 SRS1426240 GSM2144513 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144513 GEO Accession GSM2144513 SRX1748450 GSM2144514 SRP074582 SRS1426241 GSM2144514 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144514 GEO Accession GSM2144514 SRX1748451 GSM2144515 SRP074582 SRS1426243 GSM2144515 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144515 GEO Accession GSM2144515 SRX1748452 GSM2144516 SRP074582 SRS1426242 GSM2144516 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144516 GEO Accession GSM2144516 SRX1748453 GSM2144517 SRP074582 SRS1426244 GSM2144517 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144517 GEO Accession GSM2144517 SRX1748454 GSM2144518 SRP074582 SRS1426245 GSM2144518 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144518 GEO Accession GSM2144518 SRX1748455 GSM2144519 SRP074582 SRS1426248 GSM2144519 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144519 GEO Accession GSM2144519 SRX1748456 GSM2144520 SRP074582 SRS1426247 GSM2144520 RNA-Seq TRANSCRIPTOMIC cDNA Total RNA was isolated according to the modified Chomczynski and Sacchi protocol (1987) by using TRIzol ® Reagent (Life Technologies, USA). Briefly, frozen cell pellets from each sample were grounded with a sterile pre-chilled (4°C) mortar and pestle under liquid N2. TRIzol was added immediately to the grounded samples before they were thawed. The mixtures were transferred to sterile tubes and incubated at RT for 5 min. Chloroform with 1/5 volume of TRIzol was then added, vigorously mixed and incubated for further 2-3 min. The samples were centrifuged (12,000 × g, 15 min, 4°C) and the aqueous phases were collected. In order to remove any residual organic solvents from the samples, one additional chloroform extraction with half volume of the aqueous phase was performed. The incubation and centrifugation was repeated under the same conditions as described above. In order to precipitate RNA from the collected aqueous phases, isopropanol was added in the ½ volume and the mixtures were incubated at RT for 10 min. The precipitated RNAs were pelleted by centrifugation (12,000 × g, 10 min, 4°C), washed with 75% (v/v) ethanol, air-dried and re-suspended in RNase-free water. In order to remove genomic DNA from total RNA samples, they were further DNase-digested using RNase-Free DNase Set (Qiagen, Germany) according to the manufacturer’s instructions. After enzymatic treatment, RNA samples were purified by following subsequent steps: a) addition of the ½ volume of chloroform-IisoamylalcohlAA; b) centrifugation (12,000 × g, 5 min, 4°C); c) collection of the supernatant into the new tubes, d) addition of the 1/10 volume of sodium acetate (3M, pH 5.5) and 3 volumes of ice cold 100% (v/v) ethanol; e) overnight incubation in -20°C for RNA precipitation; f) centrifugation (12,000 × g, 15 min, 4°C), removal of supernatant and washing the RNA pellet with 75% (v/v) ethanol; g) centrifugation (12,000 × g, 15 min, 4°C); h) removal of supernatant and air-drying of RNA pellet; h) resuspension of RNA pellet in 50 µl of RNase-free water. RNA-sequencing was performed on an Illumina HiSeq 2500 sequencer (Illumina Inc., California, USA) at the Functional Genomics Center Zurich (FGCZ). Libraries were prepared using the Ribo-Zero™ rRNA Removal Kit (Bacteria) (http://www.illumina.com/products/ribo-zero-rrna-removal-bacteria.html, Epicentre an Illumina company, San Diego, USA), followed by the TruSeq Stranded total RNA Sample Prep Kit (Illumina) according to the manufacturer’s protocol. The libraries were qualitatively and quantitatively checked using a Qubit® (1.0) Fluorometer (Life Technologies Europe BV, Zug, Switzerland) and a Bioanalyzer 2100 (Agilent, Basel, Switzerland) and were subsequently normalized at 10 nM in Tris-Cl (10mM, pH 8.5) containing 0.1 % Tween20. Cluster generation was performed using the TruSeq SR Cluster Kit v4-cBot-HS (Illumina) using 8 pM of pooled normalized libraries on the cBOT and stranded sequencing of 125 bp was done using the TruSeq SBS Kit v4-HS (Illumina). Illumina HiSeq 2500 gds 302144520 GEO Accession GSM2144520