characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

text: not provided


status: PUBLIC

tag: attribute

text: Quadram Institute Bioscience

text: public

tag: Namespace:Quadram Institute Bioscience

text: COVID-19 Genomics UK Consortium

text: Quadram Institute Bioscience

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

text: not provided


text: public

tag: Namespace:University College London, Great Ormond Street Hospital for Children NHS Foundation Trust, Imperial College Healthcare NHS Trust

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University College London, Great Ormond Street Hospital for Children NHS Foundation Trust, Imperial College Healthcare NHS Trust

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: COVID-19 Genomics UK Consortium

text: not provided

text: not provided

text: United Kingdom

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


COG-UK/LOND-YYBYMUP

text: public

text: COG-UK/LOND-YYBYMUP

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

text: COG-UK/LOND-YYBYMUP

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Middle East Technical University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Middle East Technical University

text: Archaeological

text: human

characteristic: common name

text: Human remain

characteristic: description

text: Turkey

text: METU

text: Homo sapiens

text: Homo sapiens

text: Female

characteristic: sex

text: Petrous Bone


text: Middle East Technical University

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Archaeological

text: human

text: Human remain

text: Turkey

characteristic: geographic location (country and/or sea)

text: METU

text: Homo sapiens

text: Homo sapiens

text: Male

text: Petrous Bone

characteristic: title


text: public

tag: Namespace:Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University

text: ArrayExpress

characteristic: broker name

text: Protocols: Salmonella bacteria were grown as described in the growth protocol. When the culture reached an OD600 of 0.7-0.8, 30 ml were withdrawn, transferred to 125 ml Erlenmeyer flasks and 1.6 ml of 37% Formaldehyde (Alfa Aesar) were added. The culture was incubated for 30 min at room temperature with gentle agitation. This was followed by the addition of 6.8 ml of a 2.5 M glycine solution and a further 15 min incubation with gentle agitation at room temperature. Cells were centrifuged and the pellet resuspended in 24 ml of TBS buffer (50 mM Tris HCl pH7.4, 150mM NaCl). These steps were repeated once and the cells centrifuged again. Overnight cultures of Salmonella bacteria (inoculated from single colonies) were diluted 1:100 in LB broth or in LB broth supplemented with 0.1% ARA or 0.1% ARA + 0.4 µg/ml AHTc and grown with shaking (170 rpm) at 37°C to an OD600 of 0.7-0.8. Bacterial pellets were resuspended in 0.5 ml of Lysis buffer (50mM Tris pH 7.4, 150mM NaCl, 1mM EDTA supplemented with cOmplete™ Mini Protease Inhibitor cocktail (Sigma-Aldrich). Then, 3 µl of Ready-Lyse™ Lysozyme solution, 25 000 – 40 000 U/µl (Lucigen R1804M) were added and incubated on ice for 10 min, followed by the addition of 25 µl of 25% Triton and 450 µl of Lysis buffer. Cells were disrupted in a Covaris 220 focused ultrasonicator (Peak Incidence = 140W; Duty Factor = 5; Cycles per burst = 200). This step was followed by 10 min centrifugation at 16 000 rcf at 4°C. After removing aliquots for “INPUT” controls, supernatants (0.9 ml) were treated overnight with Anti-Flag M2 affinity Gel (Sigma A2220, 40 µl of slurry per sample) on a gyratory wheel at 8°C. Next day, beads were washed in the cold with 500 µl of TBS plus 0.05% Tween 20 for 10 minutes, followed by four TBS washes, of 10 minute each. The elution of 3xFLAG-H-NS DNA complex from the beads was accomplished as follows: 3xFLAG peptide solution (prepared according to Sigma Aldrich instructions) was diluted with TBS (3 µl of 3xFLAG peptide concentrated solution per 100 µl of TBS) and an aliquot of 2.5 times volume (relative to beads) of the peptide-TBS solution was added on top of the beads. Tubes were incubated for 1 hour on the gyratory wheel at 8°C. Samples were centrifuged briefly and supernatant transferred to a clean tube. Inputs as well as samples were treated with Proteinase K (2.5 µl of 2mg/ml solution) at 65°C overnight. DNA was cleaned using Qiagen Mini-elute reaction clean up kit ChIP DNA fragments were end-repaired and dA-tailed (NEB#E7595), Illumina TruSeq adapters were ligated (NEB#E6040) and libraries were amplified with Kapa Hifi polymerase (Kapa Biosystem #KK2103). Final libraries quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.

text: ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA hns-3xFLAG-FRT-kan-FRT

characteristic: genotype

text: Lysogeny Broth (LB) with arabinose

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

text: whole organism

characteristic: organism part

text: NusG depletion

characteristic: phenotype

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Integrative Biology of the Cell (I2BC), CNRS, Paris-Saclay University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Lysogeny Broth (LB) with arabinose

text: not applicable

characteristic: organism

text: whole organism

text: NusG depletion


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: Lysogeny Broth (LB)

text: not applicable

text: whole organism

text: wild type


text: public

text: ArrayExpress

characteristic: broker name

text: ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan hns-3xFLAG-FRT

characteristic: genotype

text: Lysogeny Broth (LB) with arabinose and anhydrotetracycline

characteristic: growth condition

text: not applicable

text: whole organism

text: SPI-1 inactivation; NusG depletion; Ptet activation

characteristic: title


text: public

text: ArrayExpress

text: Lysogeny Broth (LB)

text: not applicable

characteristic: isolate

text: whole organism

characteristic: organism part

text: SPI-1 inactivation

characteristic: phenotype

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: Protocols: Overnight bacterial cultures in LB broth were diluted 1:200 in the same medium - or in LB broth supplemented with 0.1% ARA or 0.4 µg/ml Anhydrotetracycline (AHTc) or both drugs where appropriate - and grown with shaking at 37°C to an OD600 = 0.7 to 0.8. Cultures (4 ml) were rapidly centrifuged and resuspended in 0.6 ml ice-cold REB buffer (20 mM Sodium Acetate pH 5.0, 10% sucrose). RNA was purified by sequential extraction with one volume (0.6 ml) of hot acid phenol, phenol-chloroform 1:1 mixture and chloroform. Following overnight ethanol precipitation at -20°C and centrifugation, the RNA pellet was resuspended in 20 µl of H2O. Three samples were prepared from independent biological replicates for each strain and condition. RNA yields, measured by Nanodrop reading, typically ranged between 2 and 3 µg/µl. RNA (1 µg) was combined with 1 µl of a mixture of up to four gene-specific primers, 5 µM each (including AI41 (hilD), AI48 (prgH) and AJ33 (ompA)), and 1 µl of 10 mM dNTPs in a 6 µl final volume. After a 5 min treatment at 70°C (in a Thermocycler), samples were quickly cooled on ice. Each sample were then mixed with 2.5 µl of Template Switching Buffer (4x), 0.5 µl of 75 µl of Template Switching Oligonucleotide (TSO) and 1 µl of Template Switching RT Enzyme Mix in a final volume of 10 µl. Reverse transcription was carried out for 90 min at 42°C, followed by a 5 min incubation at 85°C. The cDNAs were amplified in parallel with a common forward primer (AJ38, annealing to the TSO) and a reverse primer specific for the region being analyzed and carrying a treatment-specific index sequence. PCR reactions were set up according to New England Biolabs PCR protocol for Q5 Hot Start High-Fidelity DNA polymerase in a final volume of 50 µl (using 1 µl of the above cDNA preparation per reaction).

text: ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA

text: Lysogeny Broth (LB) with arabinose

text: not applicable

text: whole organism

text: NusG depletion


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: Lysogeny Broth (LB)

text: not applicable

characteristic: organism

text: whole organism

text: wild type


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry hilA::gfpSF ∆K28-kan

text: Lysogeny Broth (LB) with arabinose

text: not applicable

text: whole organism

text: NusG depletion


text: public

text: ArrayExpress

characteristic: broker name

characteristic: genotype

text: Lysogeny Broth (LB)

characteristic: growth condition

text: not applicable

text: whole organism

text: wild type

characteristic: title


text: public

text: ArrayExpress

text: ∆[Gifsy-1] ∆[Gifsy-2] ∆[araBAD]::gtgR-P^G2R-nusG-cat ∆[nusG]::aadA ∆[hisGDCBHAFIE]::P^Tac-mCherry ∆[sitA-prgH332]::tetR-P^tetA hilA::gfpSF ∆K28-kan

text: Lysogeny Broth (LB) with anhydrotetracycline

text: not applicable

characteristic: isolate

text: whole organism

characteristic: organism part

text: SPI-1 inactivation; Ptet activation

characteristic: phenotype

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: Lysogeny Broth (LB) with arabinose

text: not applicable

text: whole organism

text: SPI-1 inactivation; NusG depletion


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11419:MA14358-1a_plusARA_plusAHTc

text: ArrayExpress

text: not applicable

characteristic: organism

text: whole organism


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: Lysogeny Broth (LB)

text: not applicable

text: whole organism

text: SPI-1 inactivation


text: public

text: E-MTAB-11419:MA14358-1b_plusARA_plusAHTc

text: ArrayExpress

characteristic: broker name

characteristic: genotype

characteristic: growth condition

text: not applicable

text: whole organism

characteristic: title


text: public

text: ArrayExpress

text: not applicable

characteristic: isolate

text: whole organism

characteristic: organism part

characteristic: phenotype

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-11419:MA14358-3a_plusARA_plusAHTc

text: ArrayExpress

text: not applicable

text: whole organism


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11419:MA14358-3b_plusARA_plusAHTc

text: ArrayExpress

text: not applicable

characteristic: organism

text: whole organism


text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11419:MA14358-4a_plusARA_plusAHTc

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: not applicable

text: whole organism


text: public

text: E-MTAB-11419:MA14358-4b_plusARA_plusAHTc

text: ArrayExpress

characteristic: broker name

characteristic: genotype

characteristic: growth condition

text: not applicable

text: whole organism

characteristic: title


text: Cancer Research UK Beatson Institute

text: public

tag: Namespace:Cancer Research UK Beatson Institute

unit: year

characteristic: age

text: ArrayExpress

text: mesenchymal stem cell of the bone marrow

text: human

characteristic: common name

text: Protocols: MSCs were seeded at 10,000 cells/cm2 in twelve-well plates in Plasmax. After 24h, media were renewed with fresh Plasmax, supplemented with 10% dialyzed FBS and antibiotics, and cells were incubated at 21% or 1% of O2. After further 48h, cells were harvested for RNA extraction samples were processed using the QIAshredder/RNeasy Mini Kit (Qiagen) Libraries for cluster generation and DNA sequencing were prepared using Illumina TruSeq RNA Library Preparation Kit. Quality and quantity of the DNA libraries were assessed on an Agilent 2200 TapeStation (D1000 screentape) and Qubit (Thermo Fisher Scientific), respectively.

text: juvenile stage

characteristic: developmental stage

text: normal

characteristic: disease

text: hypoxia

characteristic: environmental stress

text: wild type genotype

text: Plasmax 10% dFBS

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: oxygen, 1 percent

characteristic: stimulus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Beatson Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

text: juvenile stage

text: normal

text: hypoxia

text: wild type genotype

text: Plasmax 10% dFBS

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: female

text: oxygen, 1 percent


text: Cancer Research UK Beatson Institute

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

characteristic: description

text: juvenile stage

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Plasmax 10% dFBS

characteristic: growth condition

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: Homo sapiens

text: male

text: oxygen, 21 percent

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Beatson Institute

text: public

text: ArrayExpress

text: human

text: juvenile stage

text: normal

characteristic: environmental stress

text: wild type genotype

text: Plasmax 10% dFBS

characteristic: individual

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

text: oxygen, 21 percent

characteristic: stimulus


text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:ROTHAMSTED RESEARCH

characteristic: Submitter Id

characteristic: collection date

text: uncultured Pantoea sp.

characteristic: common name

text: Genome assembly of Pantoea sp. endosymbiont of Nezara viridula from the Pest Genomics Initiative. Single individual CLR Nezara viridula genome assembly using Falcon with haplotig removal. Manual curation and Hi-C to scaffold to chromosome level. Pilon used for error correction so may be some minor gains using freebayes to update. The result was a very good assembly.

text: France

characteristic: geographic location (country and/or sea)

text: uncultured Pantoea sp.

characteristic: organism

text: uncultured Pantoea sp.


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Yokenella regensburgei

text: Genome assembly of Yokenella_regensburgei endosymbiont of Nezara viridula from the Pest Genomics Initiative. Single individual CLR Nezara viridula genome assembly using Falcon with haplotig removal. Manual curation and Hi-C to scaffold to chromosome level. Pilon used for error correction so may be some minor gains using freebayes to update. The result was a very good assembly.

characteristic: description

text: France

text: Yokenella regensburgei

text: Yokenella regensburgei

characteristic: title


text: UNIVERSITY OF NEW SOUTH WALES

text: public

tag: Namespace:UNIVERSITY OF NEW SOUTH WALES

text: human

text: Homo sapiens

text: Homo sapiens

text: Fecal


text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

characteristic: broker name

text: Public Health Agency of Canada

text: Canada

text: not provided

characteristic: host health state

text: not provided

characteristic: host scientific name

characteristic: isolate

text: Food (meat)

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

text: Canada

text: not provided

text: Gallus gallus domesticus

text: Chicken

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

characteristic: collection date

text: Canada

text: not provided

text: Bos taurus

text: Food (meat)

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

text: Canada

characteristic: geographic location (country and/or sea)

text: not provided

text: Meleagris gallopavo

text: Food (meat)

text: Escherichia coli

characteristic: organism

text: Escherichia coli


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

text: Canada

text: not provided

text: Sus scrofa

text: Pig

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

characteristic: broker name

text: Public Health Agency of Canada

text: Canada

text: not provided

text: Gallus gallus domesticus

text: Food (meat)

text: Escherichia coli

text: Escherichia coli

characteristic: title


text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: University of Manitoba

text: Canada

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Human

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

characteristic: INSDC center name

text: public

text: Quadram Institute Bioscience

text: University of Manitoba

text: Canada

text: not provided

text: Homo sapiens

characteristic: isolate

text: Human

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Quadram Institute Bioscience

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Quadram Institute Bioscience

text: University of Manitoba

text: Canada

text: not provided

text: Homo sapiens

text: Human

text: Citrobacter europaeus

text: Citrobacter europaeus


text: Quadram Institute Bioscience

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

text: Canada

text: not provided

text: Sus scrofa

text: Food (meat)

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

characteristic: Submitter Id

text: Quadram Institute Bioscience

text: Public Health Agency of Canada

characteristic: collection date

text: Canada

text: not provided

text: Meleagris gallopavo

text: Turkey

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-CHECKLIST

text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

characteristic: geographic location (country and/or sea)

text: not provided

text: Canis lupus familiaris

text: Dog

text: Escherichia coli

text: Escherichia coli


characteristic: ENA-FIRST-PUBLIC

text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

text: Sus scrofa

text: Pig

text: Escherichia coli

characteristic: organism

text: Escherichia coli


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

text: Homo sapiens

text: Human

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

characteristic: broker name

text: University of Guelph

text: Canada

text: not provided

text: Homo sapiens

text: Human

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: title


text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

characteristic: host health state

text: Canis lupus familiaris

characteristic: host scientific name

text: Dog

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: Quadram Institute Bioscience

characteristic: INSDC center name

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

text: Equus caballus

characteristic: isolate

text: Horse

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: Quadram Institute Bioscience

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

text: Gallus gallus domesticus

text: Chicken

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Quadram Institute Bioscience

text: University of Guelph

text: Canada

text: not provided

text: Bos taurus

text: Cattle

text: Escherichia coli

text: Escherichia coli


text: Quadram Institute Bioscience

text: public

characteristic: Submitter Id

text: Quadram Institute Bioscience

text: University of Guelph

characteristic: collection date

text: Canada

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text: public

text: Quadram Institute Bioscience

text: University of Guelph

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text: Dog

text: Proteus mirabilis

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characteristic: ENA-FIRST-PUBLIC

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text: public

text: Quadram Institute Bioscience

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text: Klebsiella oxytoca


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characteristic: broker name

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text: Canada

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text: Anses Laboratoire de Lyon

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characteristic: Submitter Id

text: Quadram Institute Bioscience

text: Anses Laboratoire de Lyon

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text: France

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text: public

text: Quadram Institute Bioscience

text: Anses Laboratoire de Lyon

text: France

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text: Klebsiella pneumoniae

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text: public

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text: France

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text: Quadram Institute Bioscience

text: public

text: Quadram Institute Bioscience

text: CHU Clermont-ferrand

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text: Human

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text: Human

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text: public

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text: public

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text: Pig

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text: Patient ID 4 sample A

characteristic: description

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GUH

text: public

text: Patient ID 12 sample A

text: terrestrial

characteristic: environment (biome)

text: organic

characteristic: environment (feature)

text: microbial mat

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq


text: GUH

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Patient ID 7 sample C

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq


characteristic: External Id

text: GUH

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: Patient ID 15 sample C

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GUH

text: public

characteristic: Submitter Id

characteristic: collection date

text: Patient ID 6 sample B

characteristic: description

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq

characteristic: title


text: GUH

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Patient ID 14 sample B

text: terrestrial

characteristic: environment (biome)

text: organic

characteristic: environment (feature)

text: microbial mat

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq


characteristic: External Id

text: GUH

characteristic: INSDC center name

text: public

text: Patient ID 5 sample A

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GUH

text: public

characteristic: SRA accession

text: Patient ID 13 sample A

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method


text: GUH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: collection date

text: Patient ID 8 sample C

characteristic: description

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq

characteristic: title


characteristic: External Id

text: GUH

characteristic: INSDC center name

text: public

text: Patient ID 16 sample C

text: terrestrial

characteristic: environment (biome)

text: organic

characteristic: environment (feature)

text: microbial mat

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GUH

text: public

text: Patient ID 7 sample B

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: metagenome

text: metagenome

text: Illumina MiSeq


text: GUH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Patient ID 15 sample B

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method


characteristic: External Id

text: GUH

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: collection date

text: Patient ID 6 sample A

characteristic: description

text: terrestrial

text: organic

text: microbial mat

text: Switzerland

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq

characteristic: title


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: GUH

text: public

text: Patient ID 14 sample A

text: terrestrial

characteristic: environment (biome)

text: organic

characteristic: environment (feature)

text: microbial mat

characteristic: environment (material)

text: Switzerland

characteristic: geographic location (country and/or sea)

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: Illumina MiSeq


characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Universite de Bordeaux, CNRS, UMR 5199 PACEA

text: human

characteristic: common name

text: Archaeological sample

text: Homo sapiens

text: Homo sapiens

text: Iron Age Individual


characteristic: Checklist

text: UCL

text: public

characteristic: SRA accession

characteristic: allo

text: feces

text: feces

text: feces

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: feces metagenome

characteristic: organism

text: yes

characteristic: patient

text: Gut microbiota and metabolome in pediatric stem cell transplantation

characteristic: project name

text: feces metagenome


characteristic: ENA first public

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UCL

characteristic: INSDC center name

text: public

characteristic: Submitter Id

characteristic: description

text: feces

characteristic: environment (biome)

text: feces

text: feces

text: United Kingdom

text: human-gut

text: metagenome

text: feces metagenome

text: no

text: feces metagenome

characteristic: sequencing method

characteristic: title


characteristic: Checklist

text: UCL

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: allo

text: feces

text: feces

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: human-gut

text: metagenome

text: feces metagenome

text: feces metagenome


characteristic: ENA first public

text: UCL

text: public

text: feces

text: feces

text: feces

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: feces metagenome

characteristic: organism

characteristic: project name

text: feces metagenome


text: Muscle

characteristic: ArrayExpress-PHENOTYPE

text: unknown

characteristic: ArrayExpress-SEX

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Unknown

characteristic: GENDER

text: SC

characteristic: INSDC center name

text: public

text: Muscle

characteristic: PHENOTYPE

characteristic: Submitter Id

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus


characteristic: ENA first public

text: UNIVERSITY HOHENHEIM

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY HOHENHEIM

text: Feed residue at day 13 from 24h bag, Treatment 2 Run 2 Heat pump 2

characteristic: description

text: bovine gut metagenome

text: bovine gut metagenome

text: Feed residue

characteristic: title


Mold vs. Dust

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: Mold vs. Dust

tag: Namespace:Department of Biosciences, University of Oslo

text: Fungal DNA metabarcoding library of mold and dust samples from buildings. Molds growing on damaged materials (48) and dust samples (42) were collected using sterile swabs from buildings with moisture problems in Oslo. Internal Transcribed Spacer 2 (ITS2) amplicons produced using the primers gITS7 and ITS4.

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

text: Oslo

characteristic: geographic location (region and locality)

text: dust metagenome

characteristic: organism

text: dust metagenome

text: Fungal DNA metabarcoding library (ITS2) for mold and dust samples from buildings


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

characteristic: cultivar

text: Protocols: To minimize biological variation due to sampling error, three biological replicates of each ZjPCKpro:dTALE1-STAP:GUS transgenic event were grown. T2 seed derived from three homozygous T1 lines for each independent insertion event were used – i.e. STAP4 - lines 4.2, 4.5, 4.6; STAP45 - lines 17.3, 17.5, 17.9; STAP56 - lines 21.3, 21.5, 21.8; and STAP62 - lines 23.1, 23.3, 23.8 & lines 24.3, 24.6, 24.8. Seed were sterilized and germinated on MS-hyg media (2.15 g/L MS salts & vitamins, 15 g/L sucrose, 0.5 g/L 2-(N-morpholino) ethanesulfonic acid (MES) pH 5.8, 2 g/L phytagel, 20 mg/L hygromycin) in a growth cabinet with a 16 h light/8 h dark photoperiod, light intensity of 150 μmol photons m−2 s−1, 24oC constant temperature and relative humidity of 60%. After 7 days, plants were transferred into 0.5 L pots with soil and grown in the controlled environment chamber until the 4th leaf was fully expanded. Leaf tissue (0.5 cm2) from the mid-distal leaf blade portion of the 4th fully expanded leaf was collected from ten plants per line, pooled into a 2 mL centrifuge tube, frozen in liquid N2 and stored at minus 80oC. For each line, five technical replicate pools were obtained. Samples were collected between 9am and 11am on the same day. Frozen samples were homogenized using a TissueLyser II. For dTALE2-STAP2:GUS lines, T1 and wild-type seeds were sterilized and germinated in soil at 28°C with 16 h light (400 μmol photons m−2 s−1) and 8 h dark cycle. Two independent T1 lines each of ZjPCKpro:dTALE2-STAP2.4:GUS and ZmPEPCpro:dTALE2-STAP2.4:GUS were grown, plus one T1 line of ZmPEPCpro:mTurquoise-STAP2.4:GUS. DNA was extracted from leaf 2 of 21 day old seedlings for genotyping by PCR, using HptF: CGCAAGGAATCGGTCAATACA and HptR: GATGCCTCCGCTCGAAGTAG primers to amplify the hpt transgene sequence. Plants with confirmed transgene insertions were selected for RNAseq analysis. For each T1 line, leaf 4 was collected from three individual 21 day old seedlings. For the dTALE1 lines RNA was extracted using an RNeasy Plant Mini Kit. DNA was removed from the samples using an Ambion TURBO DNA free kit and RNA quality was determined using a NanoDrop. For the dTALE2 lines RNA was extracted using Trizol reagent (Invitrogen, Waltham, Massachusetts, US) and the RNeasy Plant Mini Kit. The quality of total RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, US) by the Institute of Molecular Biology Genomics Core at Academia Sinica. library construction was performed by BGI Tech Solutions Co., Limited (Tai Po, N.T., Hongkong)

text: leaf production stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_3_pool_1

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

characteristic: description

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_3_pool_2

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_3_pool_3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

characteristic: cultivar

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_3_pool_4

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_3_pool_5

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_5_pool_1

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: description

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_5_pool_2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_5_pool_3

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_5_pool_4

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_5_pool_5

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

characteristic: description

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_9_pool_1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_9_pool_2

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_9_pool_3

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_9_pool_4

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_45_T0_17_T1_9_pool_5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

characteristic: description

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_2_pool_1

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_2_pool_2

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: Protocols: To minimize biological variation due to sampling error, three biological replicates of each ZjPCKpro:dTALE1-STAP:GUS transgenic event were grown. T2 seed derived from three homozygous T1 lines for each independent insertion event were used – i.e. STAP4 - lines 4.2, 4.5, 4.6; STAP45 - lines 17.3, 17.5, 17.9; STAP56 - lines 21.3, 21.5, 21.8; and STAP62 - lines 23.1, 23.3, 23.8 & lines 24.3, 24.6, 24.8. Seed were sterilized and germinated on MS-hyg media (2.15 g/L MS salts & vitamins, 15 g/L sucrose, 0.5 g/L 2-(N-morpholino) ethanesulfonic acid (MES) pH 5.8, 2 g/L phytagel, 20 mg/L hygromycin) in a growth cabinet with a 16 h light/8 h dark photoperiod, light intensity of 150 μmol photons m−2 s−1, 24oC constant temperature and relative humidity of 60%. After 7 days, plants were transferred into 0.5 L pots with soil and grown in the controlled environment chamber until the 4th leaf was fully expanded. Leaf tissue (0.5 cm2) from the mid-distal leaf blade portion of the 4th fully expanded leaf was collected from ten plants per line, pooled into a 2 mL centrifuge tube, frozen in liquid N2 and stored at minus 80oC. For each line, five technical replicate pools were obtained. Samples were collected between 9am and 11am on the same day. Frozen samples were homogenized using a TissueLyser II. For dTALE2-STAP2:GUS lines, T1 and wild-type seeds were sterilized and germinated in soil at 28°C with 16 h light (400 μmol photons m−2 s−1) and 8 h dark cycle. Two independent T1 lines each of ZjPCKpro:dTALE2-STAP2.4:GUS and ZmPEPCpro:dTALE2-STAP2.4:GUS were grown, plus one T1 line of ZmPEPCpro:mTurquoise-STAP2.4:GUS. DNA was extracted from leaf 2 of 21 day old seedlings for genotyping by PCR, using HptF: CGCAAGGAATCGGTCAATACA and HptR: GATGCCTCCGCTCGAAGTAG primers to amplify the hpt transgene sequence. Plants with confirmed transgene insertions were selected for RNAseq analysis. For each T1 line, leaf 4 was collected from three individual 21 day old seedlings. For the dTALE1 lines RNA was extracted using an RNeasy Plant Mini Kit. DNA was removed from the samples using an Ambion TURBO DNA free kit and RNA quality was determined using a NanoDrop. For the dTALE2 lines RNA was extracted using Trizol reagent (Invitrogen, Waltham, Massachusetts, US) and the RNeasy Plant Mini Kit. The quality of total RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, US) by the Institute of Molecular Biology Genomics Core at Academia Sinica. library construction was performed by BGI Tech Solutions Co., Limited (Tai Po, N.T., Hongkong)

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_2_pool_3

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_2_pool_4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_2_pool_5

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_5_pool_1

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_5_pool_2

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_5_pool_3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_5_pool_4

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_5_pool_5

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_6_pool_1

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_6_pool_2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_6_pool_3

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_6_pool_4

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_4_T0_4_T1_6_pool_5

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_3_pool_1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_3_pool_2

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_3_pool_3

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_3_pool_4

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: Protocols: To minimize biological variation due to sampling error, three biological replicates of each ZjPCKpro:dTALE1-STAP:GUS transgenic event were grown. T2 seed derived from three homozygous T1 lines for each independent insertion event were used – i.e. STAP4 - lines 4.2, 4.5, 4.6; STAP45 - lines 17.3, 17.5, 17.9; STAP56 - lines 21.3, 21.5, 21.8; and STAP62 - lines 23.1, 23.3, 23.8 & lines 24.3, 24.6, 24.8. Seed were sterilized and germinated on MS-hyg media (2.15 g/L MS salts & vitamins, 15 g/L sucrose, 0.5 g/L 2-(N-morpholino) ethanesulfonic acid (MES) pH 5.8, 2 g/L phytagel, 20 mg/L hygromycin) in a growth cabinet with a 16 h light/8 h dark photoperiod, light intensity of 150 μmol photons m−2 s−1, 24oC constant temperature and relative humidity of 60%. After 7 days, plants were transferred into 0.5 L pots with soil and grown in the controlled environment chamber until the 4th leaf was fully expanded. Leaf tissue (0.5 cm2) from the mid-distal leaf blade portion of the 4th fully expanded leaf was collected from ten plants per line, pooled into a 2 mL centrifuge tube, frozen in liquid N2 and stored at minus 80oC. For each line, five technical replicate pools were obtained. Samples were collected between 9am and 11am on the same day. Frozen samples were homogenized using a TissueLyser II. For dTALE2-STAP2:GUS lines, T1 and wild-type seeds were sterilized and germinated in soil at 28°C with 16 h light (400 μmol photons m−2 s−1) and 8 h dark cycle. Two independent T1 lines each of ZjPCKpro:dTALE2-STAP2.4:GUS and ZmPEPCpro:dTALE2-STAP2.4:GUS were grown, plus one T1 line of ZmPEPCpro:mTurquoise-STAP2.4:GUS. DNA was extracted from leaf 2 of 21 day old seedlings for genotyping by PCR, using HptF: CGCAAGGAATCGGTCAATACA and HptR: GATGCCTCCGCTCGAAGTAG primers to amplify the hpt transgene sequence. Plants with confirmed transgene insertions were selected for RNAseq analysis. For each T1 line, leaf 4 was collected from three individual 21 day old seedlings. For the dTALE1 lines RNA was extracted using an RNeasy Plant Mini Kit. DNA was removed from the samples using an Ambion TURBO DNA free kit and RNA quality was determined using a NanoDrop. For the dTALE2 lines RNA was extracted using Trizol reagent (Invitrogen, Waltham, Massachusetts, US) and the RNeasy Plant Mini Kit. The quality of total RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, US) by the Institute of Molecular Biology Genomics Core at Academia Sinica. library construction was performed by BGI Tech Solutions Co., Limited (Tai Po, N.T., Hongkong)

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_3_pool_5

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_5_pool_1

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_5_pool_2

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_5_pool_3

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_5_pool_4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_5_pool_5

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_8_pool_1

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_8_pool_2

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_8_pool_3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_8_pool_4

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_56_T0_21_T1_8_pool_5

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_62_T0_23_T1_1_pool_1

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

characteristic: organism

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


characteristic: ENA-CHECKLIST

characteristic: External Id

text: OXFORD

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_62_T0_23_T1_1_pool_2

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group

characteristic: title


text: OXFORD

characteristic: INSDC center name

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_62_T0_23_T1_1_pool_3

text: ArrayExpress

text: Japanese rice

text: Kitaake

characteristic: cultivar

characteristic: description

text: leaf production stage

characteristic: developmental stage

text: not applicable

characteristic: isolate

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group


text: OXFORD

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_62_T0_23_T1_1_pool_4

characteristic: Submitter Id

text: ArrayExpress

text: Japanese rice

text: Kitaake

text: leaf production stage

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

characteristic: organism part

text: Oryza sativa Japonica Group


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OXFORD

characteristic: INSDC first public

text: public

text: E-MTAB-11446:ZjPCKpro_dTALE1_STAP_62_T0_23_T1_1_pool_5

text: ArrayExpress

text: Japanese rice

characteristic: common name

text: Kitaake

text: leaf production stage

characteristic: genotype

text: not applicable

text: Oryza sativa Japonica Group

text: Oryza sativa Japonica Group

text: vascular leaf

text: Oryza sativa Japonica Group