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text: HoloFood

characteristic: project

text: HoloFood Salmon - Trial C Metagenome

characteristic: project name

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text: Shield

characteristic: sample storage buffer

text: 2ml E-matrix

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text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

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text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: sequencing method

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characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

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text: public

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characteristic: SRA accession

characteristic: Submitter Id

text: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA;AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

characteristic: adapters

characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC14.18 from tank SC14 with treatment Spurv

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

characteristic: host diet

text: Spurv: SC Ensilaged blue mussel 10.0%

characteristic: host diet treatment

characteristic: host diet treatment concentration

text: Wounded:-

characteristic: host disease status

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characteristic: host length

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characteristic: host storage container

characteristic: host storage container pH

characteristic: host storage container temperature

text: size fractionation

text: D-rex protocol

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text: Shield

text: 2ml E-matrix

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characteristic: title


characteristic: ENA-CHECKLIST

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text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

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text: public

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text: fish gut metagenome

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text: Salmon metagenomic data from Distal gut content; animal SC14.19 from tank SC14 with treatment Spurv

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

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text: Dønna; Nordland county

text: Distal gut content

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text: Spurv: SC Ensilaged blue mussel 10.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: Spurv

characteristic: host subject id

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text: Plant and Animal Whole Genome library (350bp)

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characteristic: description

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characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: description

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characteristic: host subject id

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characteristic: geographic location (country and/or sea)

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text: Wounded:-

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characteristic: host body site

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characteristic: host disease status

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characteristic: geographic location (latitude)

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text: Distal gut content

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text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

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text: LetSea Tank: And

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characteristic: geographic location (region and locality)

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characteristic: host body site

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characteristic: host common name

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characteristic: host disease status

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characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

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text: And: SC Ensilaged blue mussel 0.0%

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text: LetSea Tank: And

characteristic: host subject id

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characteristic: library name

text: size fractionation

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: fish gut metagenome

text: HoloFood

characteristic: project

text: HoloFood Salmon - Trial C Metagenome

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characteristic: sample storage buffer

text: 2ml E-matrix

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text: UCPH

characteristic: sample storage location

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characteristic: sequencing method

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

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characteristic: INSDC center name

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characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC15.11 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

characteristic: host diet

text: And: SC Ensilaged blue mussel 0.0%

characteristic: host diet treatment

characteristic: host diet treatment concentration

text: Wounded:-

characteristic: host disease status

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characteristic: host length

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characteristic: host scientific name

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characteristic: host storage container pH

characteristic: host storage container temperature

text: size fractionation

text: D-rex protocol

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text: 2ml E-matrix

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characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: collection date

text: fish gut metagenome

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text: Salmon metagenomic data from Distal gut content; animal SC15.12 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

text: Atlantic salmon

text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: And

characteristic: host subject id

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text: Plant and Animal Whole Genome library (350bp)

characteristic: library name

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characteristic: description

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characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

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text: And: SC Ensilaged blue mussel 0.0%

characteristic: host diet treatment

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text: Wounded:-

characteristic: host disease status

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characteristic: host length

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characteristic: host storage container pH

characteristic: host storage container temperature

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characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: common name

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characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

text: Atlantic salmon

text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: And

characteristic: host subject id

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characteristic: library name

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characteristic: description

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

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characteristic: host diet treatment

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text: Wounded:-

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

text: Atlantic salmon

text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

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characteristic: description

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characteristic: geographic location (latitude)

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text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

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characteristic: host diet treatment

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text: Wounded:-

characteristic: host disease status

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

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text: And: SC Ensilaged blue mussel 0.0%

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characteristic: host body site

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text: Distal gut content

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text: And: SC Ensilaged blue mussel 0.0%

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characteristic: description

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

characteristic: host diet

text: And: SC Ensilaged blue mussel 0.0%

characteristic: host diet treatment

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text: Wounded:-

characteristic: host disease status

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characteristic: host length

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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text: Distal gut content

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text: And: SC Ensilaged blue mussel 0.0%

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text: LetSea Tank: And

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characteristic: description

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: geographic location (region and locality)

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characteristic: host body site

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

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text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: And

characteristic: host subject id

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characteristic: Submitter Id

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characteristic: collection date

text: fish gut metagenome

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text: Salmon metagenomic data from Distal gut content; animal SC15.25 from tank SC15 with treatment And

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

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characteristic: host diet

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characteristic: geographic location (latitude)

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text: And: SC Ensilaged blue mussel 0.0%

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text: HoloFood

characteristic: project

text: HoloFood Salmon - Trial C Metagenome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: 2ml E-matrix

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: sequencing method

characteristic: trial timepoint


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC15.27 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

characteristic: host diet

text: And: SC Ensilaged blue mussel 0.0%

characteristic: host diet treatment

characteristic: host diet treatment concentration

text: Wounded:-

characteristic: host disease status

characteristic: host gutted mass

characteristic: host length

text: Salmo salar

characteristic: host scientific name

text: LetSea Tank: And

characteristic: host storage container

characteristic: host storage container pH

characteristic: host storage container temperature

text: size fractionation

text: D-rex protocol

text: fish gut metagenome

characteristic: organism

text: HoloFood

text: HoloFood Salmon - Trial C Metagenome

text: Shield

text: 2ml E-matrix

text: UCPH

text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC15.28 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

text: Atlantic salmon

text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: And

characteristic: host subject id

characteristic: host taxid

characteristic: host total mass

text: Plant and Animal Whole Genome library (350bp)

characteristic: library name

text: size fractionation

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: fish gut metagenome

text: HoloFood

characteristic: project

text: HoloFood Salmon - Trial C Metagenome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: 2ml E-matrix

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: sequencing method

characteristic: trial timepoint


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC15.29 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Dønna; Nordland county

characteristic: geographic location (region and locality)

text: Distal gut content

characteristic: host body site

text: Atlantic salmon

characteristic: host common name

text: Ensilaged blue mussel protein

characteristic: host diet

text: And: SC Ensilaged blue mussel 0.0%

characteristic: host diet treatment

characteristic: host diet treatment concentration

text: Wounded:-

characteristic: host disease status

characteristic: host gutted mass

characteristic: host length

text: Salmo salar

characteristic: host scientific name

text: LetSea Tank: And

characteristic: host storage container

characteristic: host storage container pH

characteristic: host storage container temperature

text: size fractionation

text: D-rex protocol

text: fish gut metagenome

characteristic: organism

text: HoloFood

text: HoloFood Salmon - Trial C Metagenome

text: Shield

text: 2ml E-matrix

text: UCPH

text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: fish gut metagenome

characteristic: common name

text: Salmon metagenomic data from Distal gut content; animal SC15.30 from tank SC15 with treatment And

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Dønna; Nordland county

text: Distal gut content

text: Atlantic salmon

text: Ensilaged blue mussel protein

text: And: SC Ensilaged blue mussel 0.0%

text: Wounded:-

text: Salmo salar

text: LetSea Tank: And

characteristic: host subject id

characteristic: host taxid

characteristic: host total mass

characteristic: library name

text: size fractionation

characteristic: library selection

text: D-rex protocol

characteristic: nucleic acid extraction

text: fish gut metagenome

text: HoloFood

characteristic: project

text: HoloFood Salmon - Trial C Metagenome

characteristic: project name

characteristic: reference host genome for decontamination

text: Shield

characteristic: sample storage buffer

text: 2ml E-matrix

characteristic: sample storage container

text: UCPH

characteristic: sample storage location

characteristic: sample storage temperature

characteristic: sample volume or weight for DNA extraction

text: fish gut metagenome

text: Illumina Novaseq 6000

characteristic: sequencing method

characteristic: trial timepoint


text: <html>Sylvilagus floridanus </html>

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: eastern cottontail

characteristic: common name

text: Sylvilagus floridanus

characteristic: organism

text: Sylvilagus floridanus

characteristic: title


E-MTAB-11580:Sample 1

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11580:Sample 1

tag: Namespace:UNIVERSITY OF MANCHESTER

text: ArrayExpress

characteristic: broker name

text: fruit fly

text: Protocols: All stocks were grown and maintained at 20°C and raised at 25°C for experiments on standard fly food media (yeast 50g/L, glucose 78g/L, maize 72g/L, agar 8g/L, 10% nipagen in EtOH 27mL/L and proprionic acid 3mL/L). The following fly lines were used in this study, y1 w* (BDSC Stock #6599), y1 w*; P{His2Av-mRFP1}II.2 (BDSC Stock #23651). Flies carrying His-RFP were allowed to lay on apple juice agar plates in small cages for 1 hour. Embryos were dechorinated in 50% bleach (2.5% final concentration of sodium hypochlorite diluted in distilled water) for 3 minutes and washed thoroughly in distilled water. Individual embryos were carefully transferred into a droplet of halocarbon oil (Sigma-Aldrich; a mix of 700 and 27 oil at a ratio of 1:4) on a rectangular coverslip (Deltalab, 24X50mm, Nr. 1) and inverted over a cavity slide (Karl Hecht). Embryos were visualised and imaged with a Leica optigrid microscope at 20X magnification using a Texas red filter. Embryos were timed following the observation of a nuclear division, an image was taken and the embryo was immediately picked out of the oil droplet with a pipette tip and transferred to Eppendorf tubes containing 50μL TRIzol Reagent (Invitrogen). Single embryos were crushed and homogenised using a pipettetip and an additional 450uL Trizol added. Samples were immediately snap frozen in liquid nitrogen and stored at -80°C until processing for nucleic acid extraction. Ten timepoints were collected spanning early Drosophila embryonic development from nc11 through to cephalic furrow formation (Table 1). Embryos were collected 5 minutes after nuclear division for nc11 and nc12, 5 and 15 minutes following the nc13 nuclear division and every 15 minutes following the nc14 nuclear division as well as embryos that showed clear cephalic furrow formation. This yielded samples covering every 10-15 minutes through development from nc11 to cephalic furrow formation. The internuclear distance of 15-20 nuclei pairs per embryo was measured in Fiji and normalised to the whole embryo length to obtain an average internuclear distance per embryo (Figure S1A and B). This was compared to the internuclear distance of embryos of known stages to accurately confirm the nuclear cleavage stage and age of embryos. All embryos were collected at 20°C with approximate time after egg lay in minutes shown in Table 1. Three female embryos from each time point were used as replicates to make 30 individual RNAseq libraries. Samples stored in Trizol (Invitrogen) were used for RNA extraction according to the manufacturer’s protocol and resuspended in 10μL (RNA) nuclease free water. Total RNA was treated with TURBO DNA-free Kit Dnase (Invitrogen) and depleted of rRNA using the Ribo-Zero Magnetic Kit HMN/Mouse/Rat 24 Rxn (Illumina; Cat# MRZH11124) according to the manufacturer’s protocol using a low input protocol with 2-4μL rRNA removal solution yielding a 20μL final sample volume added to 90μL magnetic beads. Beads were resuspended in 35μL resuspension solution and ribo-depleted total RNA was ethanol precipitated and resuspended in 18μL FPF mix prior to RNAseq library preparation. Individual total RNAseq libraries were prepared from ribo-depleted RNA using a TruSeq stranded library prep kit (Illumina) according to the manufacturer’s protocol.

characteristic: description

text: embryo stage

characteristic: developmental stage

text: pool of 3 embryos

characteristic: individual

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

characteristic: organism part

text: Drosophila melanogaster

text: female

characteristic: sex

characteristic: strain

text: Sample 1


E-MTAB-11580:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF MANCHESTER

text: public

text: E-MTAB-11580:Sample 11

text: ArrayExpress

text: fruit fly

text: embryo stage

text: pool of 3 embryos

text: Drosophila melanogaster

text: Drosophila melanogaster

text: whole organism

text: Drosophila melanogaster

text: female

text: y1 w*; P{His2Av-mRFP1}II.2 (BDSC Stock #23651)

text: Sample 11