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text: not provided

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text: public

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text: public

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text: Original

text: Denmark

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text: public

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text: public

text: Danish Covid-19 Genome Consortium

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text: public

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text: not provided

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text: not provided


characteristic: External Id

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text: public

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

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text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

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text: Human

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text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-145608/2021

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text: public

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text: Homo sapiens

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text: not provided

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text: not provided

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text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

text: active surveillance in response to outbreak


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2020-12-21

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Syddanmark

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-38414/2021

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2021-05-10

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2020-11-16

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Sjaelland

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-139784/2021

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2020-12-28

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2020-12-07

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2021-06-28

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Human

text: n_infections=2,last_infection_date=2021-01-04

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Midtjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2021-01-11

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Sjaelland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-81888/2021

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Nordjylland

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-149366/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2020-11-30

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Sjaelland

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-198478/2021

text: not provided

characteristic: host health state

text: Homo sapiens

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: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2020-12-14

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

text: active surveillance in response to outbreak


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-175261/2021

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Sjaelland

text: Human

text: n_infections=2,last_infection_date=2020-12-21

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2020-10-19

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-214720/2021

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-106123/2021

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Syddanmark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Midtjylland

text: Human

text: n_infections=2,last_infection_date=2021-11-22

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Midtjylland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sjaelland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-70540/2021

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Sjaelland

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Syddanmark

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-147798/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Nordjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2020-12-28

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Sjaelland

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-95874/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2021-08-02

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Hovedstaden

text: Human

text: n_infections=2,last_infection_date=2020-12-07

text: not provided

characteristic: host health state

text: Homo sapiens

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


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: Submitter Id

characteristic: collection date

text: Wild boar

characteristic: description

text: Sweden

text: not provided

text: Sus scrofa

text: Wild boar

text: Salmonella enterica

text: Salmonella enterica

text: Choleraesuis

characteristic: serovar


characteristic: External Id

text: NATIONAL VETERINARY INSTITUTE (SVA)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Rapeseed cake

text: Sweden

characteristic: geographic location (country and/or sea)

text: Rapeseed cake

text: Salmonella enterica

characteristic: organism

text: Salmonella enterica

text: Choleraesuis

characteristic: title


text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

characteristic: INSDC status

text: Cattle

text: Sweden

text: not provided

characteristic: host health state

text: Bos taurus

characteristic: host scientific name

characteristic: isolate

text: Cattle

text: Salmonella enterica

text: Salmonella enterica

text: Choleraesuis


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NATIONAL VETERINARY INSTITUTE (SVA)

text: public

text: Domestic pig

text: Sweden

text: not provided

text: Sus scrofa

text: Domestic pig

text: Salmonella enterica

text: Salmonella enterica

text: Choleraesuis


text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Flies were maintained under standard lab conditions (25°C). Adult flies were collected and frozen at -20°C prior to DNA extraction. Each fly was squished and incubated at 37 °C for 30 min in Squish Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 25 mM NaCl, 0.15 mg/ml Proteinase K), followed by a clean-up with a Genomic DNA Clean Concentrator kit (Zymo Research). Sequencing libraries were prepared based on publications by Picelli et al., 2014 (Smartseq2, Nature Protocols, 9(1): 171) and Hennig et al. 2018 (G3, 8:79). In short, 0.286 ng and 0.5ng of each sample was taken into a tagmentation reaction containing 1.25 uL of Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5, 40 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn5 (previously prepared as described by Hennig et al. 2018 (G3, 8:79) and diluted to a 1:50 ratio with water). The mixture was incubated at 55 degrees for 3 minutes. After that, 1.25 uL of SDS 0.2% was added to stop the tagmentation reaction followed by a 5 minutes incubation at room temperature. The resulting fragments were then amplified by PCR using 6.75 uL of KAPA 2 X HiFi master mix, 0.75 uL of Dimethyl sulfoxide and 2.5 uL of dual indexed primers. Cycling conditions were as it follows 3 minutes at 72°C; 30 seconds at 95°C; 12 cycles of 20 seconds at 98°C, 15 seconds at 58°C, 30 seconds at 72°C; 3 minutes at 72°C. The PCR products were then purified using a magnetic SPRI bead purification (0.8X). Libraries size and molarity were assessed using Bioanalyser instrument and individual libraries were pooled. Finally, the pool was size selected using two rounds of magnetic SPRI bead purification (0.65X) and quantified using the Qbit dsDNA High Sensitivity assay.

text: adult

characteristic: developmental stage

text: generation 1

characteristic: generation

text: ethyl methanesulfonate induced mutation at G0

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly a from pool 1-1

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly b from pool 1-1

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

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text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly c from pool 1-1

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly d from pool 1-1

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

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characteristic: sex

text: frozen specimen

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characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-1

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

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text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly c from pool 2-1

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly d from pool 2-1

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

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characteristic: organism part

text: Drosophila melanogaster

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characteristic: sex

text: frozen specimen

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characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

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text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-2

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

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text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

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text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-3

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly b from pool 2-3

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

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characteristic: sex

text: frozen specimen

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characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly c from pool 2-3

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-4

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly b from pool 2-4

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-5

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly b from pool 2-5

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly c from pool 2-5

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from pool 2-6

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly b from pool 2-6

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: ArrayExpress

text: fruit fly

text: adult

text: generation 1

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: fly c from pool 2-6

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Non-mutagenized Fly0-0a_Generation1

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 1

text: VK33 inserted bicoid-EGFP

text: fly a from non-mutagenized pool

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

text: Non-mutagenized Fly0-0a_Generation1

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population1-1-1A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Flies were maintained under standard lab conditions (25°C). Adult flies were collected and frozen at -20°C prior to DNA extraction. Genomic DNA from the evolved populations was prepared using a Qiagen DNeasy Tissue Kit protocol (from Alexey Veraksa), with around 100 frozen flies (about 400 ul packed flies) per population. Sequencing libraries were prepared based on publications by Picelli et al., 2014 (Smartseq2, Nature Protocols, 9(1): 171) and Hennig et al. 2018 (G3, 8:79). In short, 1.25 ng of each sample was taken into a tagmentation reaction containing 1.25 uL of Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5, 40 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn5 (previously prepared as described by Hennig et al. 2018 (G3, 8:79) and diluted to a 1:50 ratio with water). The mixture was incubated at 55 degrees for 3 minutes. After that, 1.25 uL of SDS 0.2% was added to stop the tagmentation reaction followed by a 5 minutes incubation at room temperature. The resulting fragments were then amplified by PCR using 6.75 uL of KAPA 2 X HiFi master mix, 0.75 uL of Dimethyl sulfoxide and 2.5 uL of dual indexed primers. Cycling conditions were as it follows: 3 minutes at 72�C; 30 seconds at 95�C; 12 cycles of 20 seconds at 98�C, 15 seconds at 58�C, 30 seconds at 72�C; 3 minutes at 72�C. The PCR products were then purified using a magnetic SPRI bead purification (0.8X). Libraries size and molarity were assessed using Bioanalyser and individual libraries were pooled. Finally, the pool was size selected using two rounds of magnetic SPRI bead purification (0.65X) and quantified using the Qbit dsDNA High Sensitivity assay.

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 1-1-1A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population1-1-1A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

text: generation 7

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population1-1-2A_Generation3

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 1-1-2A, pool of around 100 flies

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population1-1-2A_Generation7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population1-1-3A_Generation3

text: ArrayExpress

text: fruit fly

text: adult

text: generation 3

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characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: population 1-1-3A, pool of around 100 flies

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: E-MTAB-11768:Population1-1-3A_Generation7

text: ArrayExpress

text: fruit fly

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text: adult

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text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

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text: Drosophila melanogaster

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text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-1-1A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-1-1A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-1-1A_Generation7

text: ArrayExpress

text: fruit fly

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text: VK33 inserted bicoid-EGFP

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text: Drosophila melanogaster

text: Drosophila melanogaster

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text: Drosophila melanogaster

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text: frozen specimen

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characteristic: strain


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characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-1-2A_Generation3

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-1-2A, pool of around 100 flies

text: Drosophila melanogaster

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text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

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text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-1-2A_Generation7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 7

text: ethyl methanesulfonate induced mutation at G0

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-2-1A_Generation3

text: ArrayExpress

text: fruit fly

text: adult

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text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: population 2-2-1A, pool of around 100 flies

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text: Drosophila melanogaster

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characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-2-1A_Generation7

text: ArrayExpress

text: fruit fly

text: Protocols: Flies were maintained under standard lab conditions (25°C). Adult flies were collected and frozen at -20°C prior to DNA extraction. Genomic DNA from the evolved populations was prepared using a Qiagen DNeasy Tissue Kit protocol (from Alexey Veraksa), with around 100 frozen flies (about 400 ul packed flies) per population. Sequencing libraries were prepared based on publications by Picelli et al., 2014 (Smartseq2, Nature Protocols, 9(1): 171) and Hennig et al. 2018 (G3, 8:79). In short, 1.25 ng of each sample was taken into a tagmentation reaction containing 1.25 uL of Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5, 40 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn5 (previously prepared as described by Hennig et al. 2018 (G3, 8:79) and diluted to a 1:50 ratio with water). The mixture was incubated at 55 degrees for 3 minutes. After that, 1.25 uL of SDS 0.2% was added to stop the tagmentation reaction followed by a 5 minutes incubation at room temperature. The resulting fragments were then amplified by PCR using 6.75 uL of KAPA 2 X HiFi master mix, 0.75 uL of Dimethyl sulfoxide and 2.5 uL of dual indexed primers. Cycling conditions were as it follows: 3 minutes at 72�C; 30 seconds at 95�C; 12 cycles of 20 seconds at 98�C, 15 seconds at 58�C, 30 seconds at 72�C; 3 minutes at 72�C. The PCR products were then purified using a magnetic SPRI bead purification (0.8X). Libraries size and molarity were assessed using Bioanalyser and individual libraries were pooled. Finally, the pool was size selected using two rounds of magnetic SPRI bead purification (0.65X) and quantified using the Qbit dsDNA High Sensitivity assay.

characteristic: description

text: adult

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-2-2A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-2-2A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-2-2A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

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characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-3-1A_Generation3

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

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text: VK33 inserted bicoid-EGFP

text: population 2-3-1A, pool of around 100 flies

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-3-1A_Generation7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-3-2A_Generation3

text: ArrayExpress

text: fruit fly

text: adult

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characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: population 2-3-2A, pool of around 100 flies

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

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characteristic: sex

text: frozen specimen

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characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

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text: E-MTAB-11768:Population2-3-2A_Generation7

text: ArrayExpress

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text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

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characteristic: title


characteristic: ENA-FIRST-PUBLIC

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text: EMBL

characteristic: INSDC last update

text: public

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text: E-MTAB-11768:Population2-4-1A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-4-1A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-4-1A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

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characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

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text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

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text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

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characteristic: strain


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characteristic: External Id

text: EMBL

characteristic: INSDC center name

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text: public

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text: E-MTAB-11768:Population2-4-2A_Generation3

text: ArrayExpress

text: fruit fly

characteristic: description

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text: ethyl methanesulfonate induced mutation at G0

text: VK33 inserted bicoid-EGFP

text: population 2-4-2A, pool of around 100 flies

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-4-2A_Generation7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

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text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-5-1A_Generation3

text: ArrayExpress

text: fruit fly

text: Protocols: Flies were maintained under standard lab conditions (25°C). Adult flies were collected and frozen at -20°C prior to DNA extraction. Genomic DNA from the evolved populations was prepared using a Qiagen DNeasy Tissue Kit protocol (from Alexey Veraksa), with around 100 frozen flies (about 400 ul packed flies) per population. Sequencing libraries were prepared based on publications by Picelli et al., 2014 (Smartseq2, Nature Protocols, 9(1): 171) and Hennig et al. 2018 (G3, 8:79). In short, 1.25 ng of each sample was taken into a tagmentation reaction containing 1.25 uL of Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5, 40 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn5 (previously prepared as described by Hennig et al. 2018 (G3, 8:79) and diluted to a 1:50 ratio with water). The mixture was incubated at 55 degrees for 3 minutes. After that, 1.25 uL of SDS 0.2% was added to stop the tagmentation reaction followed by a 5 minutes incubation at room temperature. The resulting fragments were then amplified by PCR using 6.75 uL of KAPA 2 X HiFi master mix, 0.75 uL of Dimethyl sulfoxide and 2.5 uL of dual indexed primers. Cycling conditions were as it follows: 3 minutes at 72�C; 30 seconds at 95�C; 12 cycles of 20 seconds at 98�C, 15 seconds at 58�C, 30 seconds at 72�C; 3 minutes at 72�C. The PCR products were then purified using a magnetic SPRI bead purification (0.8X). Libraries size and molarity were assessed using Bioanalyser and individual libraries were pooled. Finally, the pool was size selected using two rounds of magnetic SPRI bead purification (0.65X) and quantified using the Qbit dsDNA High Sensitivity assay.

text: adult

text: generation 3

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: population 2-5-1A, pool of around 100 flies

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-5-1A_Generation7

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-5-2A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-5-2A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-5-2A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

text: generation 7

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-6-1A_Generation15

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 15

text: VK33 inserted bicoid-EGFP

text: population 2-6-1A, pool of around 100 flies

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-6-1A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-6-1A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

text: generation 7

characteristic: generation

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Population2-6-1A_Generation9

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 9

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Population2-6-2A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 3

text: VK33 inserted bicoid-EGFP

text: population 2-6-2A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Population2-6-2A_Generation7

text: ArrayExpress

text: fruit fly

text: adult

text: generation 7

characteristic: generation

text: ethyl methanesulfonate induced mutation at G0

characteristic: genetic modification

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Non-mutagenized Population0-0-1A_Generation3

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 3

text: VK33 inserted bicoid-EGFP

text: non-mutagenized population 0-0-1A, pool of around 100 flies

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Non-mutagenized Population0-0-1A_Generation7

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

characteristic: common name

text: Protocols: Flies were maintained under standard lab conditions (25°C). Adult flies were collected and frozen at -20°C prior to DNA extraction. Genomic DNA from the evolved populations was prepared using a Qiagen DNeasy Tissue Kit protocol (from Alexey Veraksa), with around 100 frozen flies (about 400 ul packed flies) per population. Sequencing libraries were prepared based on publications by Picelli et al., 2014 (Smartseq2, Nature Protocols, 9(1): 171) and Hennig et al. 2018 (G3, 8:79). In short, 1.25 ng of each sample was taken into a tagmentation reaction containing 1.25 uL of Dimethylformamide, 1.25 uL of tagmentation buffer (40 mM Tris-HCl pH 7.5, 40 mM MgCl2) and 1.25 uL of an in-house generated and purified Tn5 (previously prepared as described by Hennig et al. 2018 (G3, 8:79) and diluted to a 1:50 ratio with water). The mixture was incubated at 55 degrees for 3 minutes. After that, 1.25 uL of SDS 0.2% was added to stop the tagmentation reaction followed by a 5 minutes incubation at room temperature. The resulting fragments were then amplified by PCR using 6.75 uL of KAPA 2 X HiFi master mix, 0.75 uL of Dimethyl sulfoxide and 2.5 uL of dual indexed primers. Cycling conditions were as it follows: 3 minutes at 72�C; 30 seconds at 95�C; 12 cycles of 20 seconds at 98�C, 15 seconds at 58�C, 30 seconds at 72�C; 3 minutes at 72�C. The PCR products were then purified using a magnetic SPRI bead purification (0.8X). Libraries size and molarity were assessed using Bioanalyser and individual libraries were pooled. Finally, the pool was size selected using two rounds of magnetic SPRI bead purification (0.65X) and quantified using the Qbit dsDNA High Sensitivity assay.

text: adult

characteristic: developmental stage

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


text: EMBL

text: public

text: E-MTAB-11768:Non-mutagenized Population0-0-2A_Generation3

text: ArrayExpress

text: fruit fly

text: adult

text: generation 3

characteristic: generation

text: VK33 inserted bicoid-EGFP

characteristic: genotype

text: non-mutagenized population 0-0-2A, pool of around 100 flies

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen

characteristic: specimen with known storage state

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: EMBL

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: E-MTAB-11768:Non-mutagenized Population0-0-2A_Generation7

text: ArrayExpress

text: fruit fly

characteristic: description

text: adult

text: generation 7

text: VK33 inserted bicoid-EGFP

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMBL

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: E-MTAB-11768:Non-mutagenized Population0-0-3A_Generation3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: adult

text: generation 3

text: VK33 inserted bicoid-EGFP

text: non-mutagenized population 0-0-3A, pool of around 100 flies

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: mixed

text: frozen specimen

characteristic: title


text: EMBL

text: public

text: E-MTAB-11768:Non-mutagenized Population0-0-3A_Generation7

text: ArrayExpress

text: fruit fly

characteristic: common name

text: adult

characteristic: developmental stage

text: generation 7

characteristic: generation

text: VK33 inserted bicoid-EGFP

characteristic: genotype

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: mixed

characteristic: sex

text: frozen specimen


characteristic: ENA-CHECKLIST

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

tag: Namespace:INSTITUT PASTEUR

text: CSF-(idiopathic)

text: Spain

characteristic: geographic location (country and/or sea)

text: human metagenome

text: human metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR

characteristic: INSDC last update

text: public

characteristic: SRA accession

text: CSF-(idiopathic)

characteristic: description

text: Spain

text: Toscana virus

characteristic: organism

text: Toscana virus


text: INSTITUT PASTEUR

text: public

characteristic: Submitter Id

text: Spain

text: human metagenome

text: human metagenome

characteristic: title


text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: public

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

text: Denmark

text: Hovedstaden

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2020-11-16

characteristic: host description

text: not provided

characteristic: host health state

text: Homo sapiens

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

text: active surveillance in response to outbreak

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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characteristic: INSDC center name

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text: public

characteristic: INSDC status

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text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (country and/or sea)

text: Syddanmark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


text: public

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

text: Nordjylland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

characteristic: host description

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

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text: public

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text: Homo sapiens

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