ERS4573797 SAMEA6846197 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846197 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S1 -TEX broker name ArrayExpress environmental stress mixed (pH, NaCl, H2O2) growth phase exponential organism part whole organism sample name E-MTAB-9075:S1 -TEX strain 3937 ERS4573798 SAMEA6846198 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846198 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S3 -TEX broker name ArrayExpress environmental stress mixed (pH, NaCl, H2O2) growth phase stationary organism part whole organism sample name E-MTAB-9075:S3 -TEX strain 3937 ERS4573799 SAMEA6846199 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846199 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S1 +TEX broker name ArrayExpress environmental stress mixed (pH, NaCl, H2O2) growth phase exponential organism part whole organism sample name E-MTAB-9075:S1 +TEX strain 3937 treatment terminator exonuclease ERS4573800 SAMEA6846200 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846200 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S3 +TEX broker name ArrayExpress environmental stress mixed (pH, NaCl, H2O2) growth phase stationary organism part whole organism sample name E-MTAB-9075:S3 +TEX strain 3937 treatment terminator exonuclease ERS4573801 SAMEA6846201 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846201 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S2 -TEX broker name ArrayExpress growth phase exponential organism part whole organism sample name E-MTAB-9075:S2 -TEX strain 3937 ERS4573802 SAMEA6846202 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846202 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S4 -TEX broker name ArrayExpress growth phase stationary organism part whole organism sample name E-MTAB-9075:S4 -TEX strain 3937 ERS4573803 SAMEA6846203 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846203 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S2 +TEX broker name ArrayExpress growth phase exponential organism part whole organism sample name E-MTAB-9075:S2 +TEX strain 3937 treatment terminator exonuclease ERS4573804 SAMEA6846204 204038 Dickeya dadantii Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics). ENA first public 2022-01-01 ENA last update 2022-01-01 External Id SAMEA6846204 INSDC center alias Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC center name Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie INSDC first public 2022-01-01T00:12:24Z INSDC last update 2022-01-01T00:12:24Z INSDC status public Submitter Id E-MTAB-9075:S4 +TEX broker name ArrayExpress growth phase stationary organism part whole organism sample name E-MTAB-9075:S4 +TEX strain 3937 treatment terminator exonuclease