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text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: kidney cell

characteristic: cell type

text: Protocols: MARC-145 cells, a derivative of the MA-104 cell line, were maintained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with L-glutamine (1 mM), antibiotics, and foetal bovine serum (FBS) (7%), at 37°C and 5% CO2. Cells were verified as mycoplasma-free by PCR (Universal Mycoplasma Detection Kit, ATCC) and deep sequencing. Cells were infected with NA PRRSV isolate SD95-21 (GenBank accession KC469618.1), or a mutant (KO2) based on this background. KO2 has been previously characterised (Fang et al., 2012; Li et al., 2014; Li et al., 2018), and has a modified nsp2 slippery sequence (G_GUU_UUU to G_GUA_UUC), a premature stop codon 5 nt downstream in the -2 frame, and several mutations in and around the conserved C-rich motif (U3886A, U3889C, C3895A, C3898G, U3899A, C3900G, C3901U, C3905U and C3907G), where all mutations are synonymous in the ORF1a reading frame. Confluent 10 cm2 dishes of MARC-145 cells were infected with WT or KO2 virus at a MOI of 5, or mock-infected. At 9 hpi, cells were washed with 5 ml warm PBS and snap-frozen in liquid nitrogen. Snap-frozen dishes were transferred to dry ice and 400 µl lysis buffer [20 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 μg/ml cycloheximide and 25 U/ml TURBO DNase (Life Technologies)] added. The dish was transferred to ice to defrost, and then cells were scraped off the plate and triturated 10 times with a 26-G needle, before cell debris was removed by centrifugation (microfuge, 4°C, 20 min) and the supernatant was harvested and stored at −70°C. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol:chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing (Chung et al., 2015). Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 19-80nt. Library amplicons were constructed using adapters based on the TruSeq small RNA adapters, with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter.

characteristic: description

text: late embryo

characteristic: developmental stage

text: normal

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text: Chlorocebus sabaeus

text: Chlorocebus sabaeus

text: kidney

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text: Chlorocebus sabaeus


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text: public

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text: Protocols: For PRRSV-1-infected cells: MA-104 cells, a cell line derived from foetal kidney tissue of the African green monkey species Chlorocebus sabaeus, were infected with a PRRSV strain derived from the Porcilis® vaccine strain (MSD Animal Health; GenBank accession KJ127878.1) but with 148 accumulated mutations (see associated publication for genome sequence). Confluent 6 cm2 dishes of MA-104 cells were infected at a multiplicity of infection (MOI) within the range 1-3. At 0 (mock) and 8 hpi cycloheximide (Sigma-Aldrich) was added to the medium (final concentration 100 µg/ml) and incubated for 2 min. Cells were rinsed with 5 ml of ice cold PBS, placed on ice, and 400 µl lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml CHX and 25 U/ml TURBO™ DNase [Life Technologies] was added drop-wise. Cells were scraped off the plate and triturated 10 times with a 26-G needle, before cell debris was removed by centrifugation (microfuge, 4°C, 20 min) and the supernatant was harvested and stored at −70°C. For PRRSV-2-infected cells: MARC-145 cells, a derivative of the MA-104 cell line, were maintained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with L-glutamine (1 mM), antibiotics, and foetal bovine serum (FBS) (7%), at 37°C and 5% CO2. Cells were verified as mycoplasma-free by PCR (Universal Mycoplasma Detection Kit, ATCC) and deep sequencing. Cells were infected with NA PRRSV isolate SD95-21 (GenBank accession KC469618.1), or a mutant (KO2) based on this background. KO2 has been previously characterised (Fang et al., 2012; Li et al., 2014; Li et al., 2018), and has a modified nsp2 slippery sequence (G_GUU_UUU to G_GUA_UUC), a premature stop codon 5 nt downstream in the -2 frame, and several mutations in and around the conserved C-rich motif (U3886A, U3889C, C3895A, C3898G, U3899A, C3900G, C3901U, C3905U and C3907G), where all mutations are synonymous in the ORF1a reading frame. Confluent 10 cm2 dishes of MARC-145 cells were infected with WT or KO2 virus at a MOI of 5, or mock-infected. For the CHX_Ribo_9hpi libraries, CHX pre-treatment and harvesting was performed at 9 hpi as described for PRRSV-1-infected cells. For all other libraries, at 3, 6, 9, or 12 hpi, cells were washed with 5 ml warm PBS and snap-frozen in liquid nitrogen. Snap-frozen dishes were transferred to dry ice and 400 µl lysis buffer (composition as described above) added. The dish was transferred to ice to defrost, and then cells were scraped and processed as described above. RNase I was added to the lysates for 45 minutes at room temperature, following which ribosomes and ribosome-protected fragments of RNA were purified by centrifugation through a sucrose cushion. RNA was extracted from the purified ribosomes by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol:chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing (Chung et al., 2015). Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was purified by 15% denaturing urea gel purification to select fragments of 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or 19-34 nt (all other samples), from which library amplicons were constructed using adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used to generate amplicons. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter.

text: late embryo

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text: Protocols: For PRRSV-1-infected cells: MA-104 cells, a cell line derived from foetal kidney tissue of the African green monkey species Chlorocebus sabaeus, were infected with a PRRSV strain derived from the Porcilis® vaccine strain (MSD Animal Health; GenBank accession KJ127878.1) but with 148 accumulated mutations (see associated publication for genome sequence). Confluent 6 cm2 dishes of MA-104 cells were infected at a multiplicity of infection (MOI) within the range 1-3. At 0 (mock) and 8 hpi cycloheximide (Sigma-Aldrich) was added to the medium (final concentration 100 µg/ml) and incubated for 2 min. Cells were rinsed with 5 ml of ice cold PBS, placed on ice, and 400 µl lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml CHX and 25 U/ml TURBO™ DNase [Life Technologies] was added drop-wise. Cells were scraped off the plate and triturated 10 times with a 26-G needle, before cell debris was removed by centrifugation (microfuge, 4°C, 20 min) and the supernatant was harvested and stored at −70°C. For PRRSV-2-infected cells: MARC-145 cells, a derivative of the MA-104 cell line, were maintained in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with L-glutamine (1 mM), antibiotics, and foetal bovine serum (FBS) (7%), at 37°C and 5% CO2. Cells were verified as mycoplasma-free by PCR (Universal Mycoplasma Detection Kit, ATCC) and deep sequencing. Cells were infected with NA PRRSV isolate SD95-21 (GenBank accession KC469618.1), or a mutant (KO2) based on this background. KO2 has been previously characterised (Fang et al., 2012; Li et al., 2014; Li et al., 2018), and has a modified nsp2 slippery sequence (G_GUU_UUU to G_GUA_UUC), a premature stop codon 5 nt downstream in the -2 frame, and several mutations in and around the conserved C-rich motif (U3886A, U3889C, C3895A, C3898G, U3899A, C3900G, C3901U, C3905U and C3907G), where all mutations are synonymous in the ORF1a reading frame. Confluent 10 cm2 dishes of MARC-145 cells were infected with WT or KO2 virus at a MOI of 5, or mock-infected. For the CHX_RNA_9hpi libraries, CHX pre-treatment and harvesting was performed at 9 hpi as described for PRRSV-1-infected cells. For all other libraries, at 3, 6, 9, or 12 hpi, cells were washed with 5 ml warm PBS and snap-frozen in liquid nitrogen. Snap-frozen dishes were transferred to dry ice and 400 µl lysis buffer (composition as described above) added. The dish was transferred to ice to defrost, and then cells were scraped and processed as described above. RNA was extracted from the lysates by proteinase K digestion (enzyme from NEB, reaction at 42 degrees for 30 minutes) followed by hot acidic phenol:chloroform extraction and ethanol precipitation. The methodologies employed were based on the original protocols of Ingolia and colleagues (Ingolia et al., 2009; Ingolia et al., 2012), except library amplicons were constructed using a small RNA cloning strategy (Guo et al., 2010) adapted to Illumina smallRNA v2 to allow multiplexing (Chung et al., 2015). Ribosomal RNA was removed using Ribo-Zero Gold rRNA removal kit (Illumina), and remaining RNA was fragmented by alkaline hydrolysis (45mM NaHCO3, 6mM Na2CO3, 1mM EDTA; 95 degrees, 15 minutes). Fragments of 25-34 nt (PRRSV-1-infected samples, CHX-pre-treated PRRSV-2- or mock-infected samples, and non-CHX-pre-treated PRRSV-2- or mock-infected 9 hpi replicate one samples) or ~50 nt (all other samples) were selected by 15% denaturing urea gel purification, from which library amplicons were constructed using adapters based on the TruSeq small RNA adapters. For all PRRSV-2-infected (or mock-infected) libraries, adapters with an additional seven random nucleotides at the 5′-end of the 3′-adapter and the 3′-end of the 5′-adapter were used. For PRRSV-1 replicate one, no random nucleotides were present on the adapters, and for PRRSV-1 replicate two, 14 random nucleotides were present at the 5′-end of the 3′-adapter.

characteristic: description

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text: Bothrioplana semperi

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text: ArrayExpress

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text: Protocols: 10 day seedlings and unopened floral bud from approximately 40 day-old plants long day conditions (16 hr light), 20 degrees Celsius Trizol ScriptSeq v2 RNA-seq Library Preparation Kit (SSV21124, Epicentre)

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characteristic: ENA-CHECKLIST

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characteristic: External Id

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: Klebsiella pneumoniae

characteristic: ArrayExpress-Species

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella oxytoca

text: SC

text: public

text: Klebsiella oxytoca

text: Klebsiella oxytoca

text: Klebsiella oxytoca


text: Escherichia coli

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text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Staphylococcus haemolyticus

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text: public

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus


text: Staphylococcus warneri

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text: public

text: Staphylococcus warneri

text: Staphylococcus warneri

text: Staphylococcus warneri


text: Staphylococcus lugdunensis

text: SC

text: public

text: Staphylococcus lugdunensis

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus


text: Acinetobacter baumannii

text: SC

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: Acinetobacter variabilis

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text: Acinetobacter variabilis

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: public

tag: Namespace:: University of Cambridge, Department of Pathology

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: Cell line maintained in DMEM. All cells were treated with doxycycline to induce viral protein expression. Trizol PARFA-Seq

characteristic: description

text: embryo

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text: normal

characteristic: disease

text: tetR (tetracycline repressor), bsd (blasticidin resistance gene), ble (zeocin resistance gene)

characteristic: genotype

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characteristic: organism part

text: Homo sapiens


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characteristic: External Id

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text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella variicola

characteristic: common name

text: Klebsiella variicola

text: Klebsiella variicola


text: Klebsiella quasipneumoniae

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text: public

text: Klebsiella quasipneumoniae

text: Klebsiella quasipneumoniae

text: Klebsiella quasipneumoniae


text: Pseudomonas stutzeri

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text: public

text: Pseudomonas stutzeri

text: Pseudomonas stutzeri

text: Pseudomonas stutzeri


text: Proteus mirabilis

text: SC

text: public

text: Proteus mirabilis

text: Proteus mirabilis

text: Proteus mirabilis


text: Acinetobacter schindleri

text: SC

text: public

text: Acinetobacter schindleri

text: Escherichia coli

text: Escherichia coli


text: Enterobacter hormaechei

text: SC

text: public

text: Enterobacter hormaechei

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella michiganensis

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text: Klebsiella michiganensis

text: Klebsiella michiganensis

text: Klebsiella michiganensis


text: Escherichia coli

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Enterococcus faecalis

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


text: Staphylococcus aureus

text: SC

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text: Staphylococcus aureus

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text: Staphylococcus aureus


text: Staphylococcus haemolyticus

text: SC

text: public

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus


text: Acinetobacter baumannii

text: SC

text: public

text: Acinetobacter baumannii

text: Acinetobacter baumannii

text: Acinetobacter baumannii


text: Acinetobacter nosocomialis

text: SC

text: public

text: Acinetobacter nosocomialis

text: Acinetobacter nosocomialis

text: Acinetobacter nosocomialis


text: Pseudomonas aeruginosa

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Salmonella enterica subsp. enterica serovar Enteritidis

text: SC

text: public


text: Salmonella diarizonae

text: SC

text: public

text: Salmonella diarizonae

text: Salmonella enterica subsp. diarizonae

text: Salmonella enterica subsp. diarizonae


text: Citrobacter freundii

text: SC

text: public

text: Citrobacter freundii

text: Citrobacter freundii

text: Citrobacter freundii


text: public

tag: Namespace:CENTRO DE INVESTIGACION Y TECNOLOGIA AGROALIMENTARIA DE ARAGON

text: Centro de Investigacion y Tecnologia Agroalimentaria de Aragon

characteristic: collected by

text: almond

text: 1-year-old Prunus dulcis shoot tip

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

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text: 41.8630563850573, -0.6526712419313184

characteristic: lat lon

text: Prunus dulcis

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characteristic: tissue type

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text: public

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characteristic: External Id

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characteristic: title


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characteristic: Submitter Id

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characteristic: ENA-CHECKLIST

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characteristic: lat lon

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characteristic: INSDC last update

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characteristic: title


text: public

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text: Prunus dulcis

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characteristic: description

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characteristic: geographic location (country and/or sea)

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text: 41.8630563850573, -0.6526712419313184

text: Prunus dulcis

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characteristic: ENA-CHECKLIST

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characteristic: geographic location (region and locality)

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characteristic: lat lon

text: Prunus dulcis

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characteristic: ENA-FIRST-PUBLIC

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text: Prunus dulcis

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characteristic: External Id

characteristic: INSDC center name

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text: 41.8630563850573, -0.6526712419313184

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characteristic: organism

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characteristic: INSDC first public

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text: Prunus dulcis

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text: CENTRO DE INVESTIGACION Y TECNOLOGIA AGROALIMENTARIA DE ARAGON

text: public

characteristic: SRA accession

characteristic: Submitter Id

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text: 1-year-old Prunus dulcis shoot tip

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characteristic: title


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text: Prunus dulcis

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characteristic: ENA-CHECKLIST

text: public

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text: Spain

characteristic: geographic location (country and/or sea)

text: Zuera, Zaragoza

characteristic: geographic location (region and locality)

text: 41.8630563850573, -0.6526712419313184

text: Prunus dulcis

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text: shoot tips

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characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

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text: 1-year-old Prunus dulcis shoot tip

text: Spain

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text: 41.8630563850573, -0.6526712419313184

characteristic: lat lon

text: Prunus dulcis

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characteristic: External Id

characteristic: INSDC center name

text: public

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text: 1-year-old Prunus dulcis shoot tip

text: Spain

text: Zuera, Zaragoza

text: 41.8630563850573, -0.6526712419313184

text: Prunus dulcis

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characteristic: tissue type

text: Lauranne-Garnem combination biological replicate 1 (RNA-Seq Illumina)


characteristic: INSDC first public

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text: public

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text: 41.8630563850573, -0.6526712419313184

text: Prunus dulcis

characteristic: organism

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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text: 41.8630563850573, -0.6526712419313184

text: Prunus dulcis

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text: shoot tips

text: Lauranne-Garnem combination biological replicate 3 (RNA-Seq Illumina)


text: public

tag: Namespace:Archaeogenomics group, Department of Biosciences, University of Oslo

text: walrus

characteristic: common name

text: Odobenus rosmarus

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text: WGS sequencing data

characteristic: title


characteristic: ENA-CHECKLIST

text: Archaeogenomics group, Department of Biosciences, University of Oslo

text: public

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text: IRHS, SPE, INRAE

characteristic: INSDC secondary accession

text: live

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: missing

text: Golden delicious

characteristic: genotype

text: missing

text: Malus domestica

text: leaf

text: leaf

characteristic: tissue

text: formulated cutin monomer extract

characteristic: treatment


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