SRX11408477 SIER_t_22 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452153 SIER_t_22 SIER_t_22 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408478 SIER_t_23 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452154 SIER_t_23 SIER_t_23 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408479 SIER_t_24 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452155 SIER_t_24 SIER_t_24 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408480 SIER_t_3 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452156 SIER_t_3 SIER_t_3 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408481 SIER_t_4 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452157 SIER_t_4 SIER_t_4 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408482 SIER_t_5 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452158 SIER_t_5 SIER_t_5 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408483 SIER_t_6 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452159 SIER_t_6 SIER_t_6 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408484 SIER_t_7 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452160 SIER_t_7 SIER_t_7 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408485 SIER_t_8 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452161 SIER_t_8 SIER_t_8 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408486 SIER_t_9 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452162 SIER_t_9 SIER_t_9 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408487 SIER_t_10 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452163 SIER_t_10 SIER_t_10 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408488 SIER_t_1 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452164 SIER_t_1 SIER_t_1 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408489 SIER_t_2 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452165 SIER_t_2 SIER_t_2 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408490 SIER_t_11 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452166 SIER_t_11 SIER_t_11 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408491 SIER_t_12 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452167 SIER_t_12 SIER_t_12 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408492 SIER_t_13 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452168 SIER_t_13 SIER_t_13 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408493 SIER_t_14 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452169 SIER_t_14 SIER_t_14 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408494 SIER_t_15 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452170 SIER_t_15 SIER_t_15 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408495 SIER_t_16 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452171 SIER_t_16 SIER_t_16 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500 SRX11408496 SIER_t_21 SRP327880 bp0 Samples were collected on day 3 post infection (3 dpi) and day 6 post infection (6 dpi), respectively Total RNA and DNA were sequentially isolated. Sampled individuals were homogenized in 300 l (3 dpi) and 600 l (6 dpi) extraction buffer, respectively. RNA was isolated using a NucleoSpin RNA purification kit (Macherey-Nagel, Dren, Germany) according to manufacturers protocol. Remaining genomic DNA was removed by digestion with TURBO DNase (Invitrogen, ThermoFischer Scientific, Paisley, United Kingdom). The Ribo-Zero magnetic kit (Epicentre Biotechnologies, Madison, WI, USA) was used to reduce the amount of bacterial-derived rRNA sequences. The NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Frankfurt am Main, Germany) was used to remove eukaryotic-derived rRNA sequences. cDNA libraries were constructed with a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs, Frankfurt am Main, Germany). To assess quality and size of the libraries samples were run on an Agilent Bioanalyzer 2100 using an Agilent High Sensitivity DNA Kit as recommended by the manufacturer (Agilent Technologies, Waldbronn, Germany). Concentration of the libraries were determined using the Qubit dsDNA HS Assay Kit as recommended by the manufacturer (Life Technologies GmbH, Darmstadt, Germany). SRS9452172 SIER_t_21 SIER_t_21 RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 2500