characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: Colombia

characteristic: geographic location (longitude)

text: Putumayo | Mocoa | Campucana

characteristic: geographic location (region and locality)

text: Tropical rainforest

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

text: Melinaea ludovica

characteristic: organism

text: THORAX

text: Melinaea ludovica

text: MALE

text: N

characteristic: title


status: PUBLIC

tag: attribute

text: Sanger Institute

text: Tree of Life Programme

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Tree of Life Programme

characteristic: Submitter Id

text: EVA VAN DER HEIJDEN

text: Sanger Institute

characteristic: collecting institution

characteristic: collection date

unit: m

characteristic: elevation

text: Colombia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

text: Putumayo | Mocoa | Campucana

text: Tropical rainforest

characteristic: habitat

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

characteristic: lifestage

text: Melinaea ludovica

text: LEG

characteristic: organism part

characteristic: project name

characteristic: sample derived from

text: Melinaea ludovica

text: MALE

characteristic: sex

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: Colombia

characteristic: geographic location (longitude)

text: Putumayo | Mocoa | Campucana

characteristic: geographic location (region and locality)

text: Tropical rainforest

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

text: Tithorea tarricina

characteristic: organism

text: HEAD | ABDOMEN

text: Tithorea tarricina

text: FEMALE

text: N

characteristic: title


text: Sanger Institute

text: Tree of Life Programme

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: EVA VAN DER HEIJDEN

text: Sanger Institute

characteristic: collecting institution

characteristic: collection date

characteristic: elevation

text: Colombia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Putumayo | Mocoa | Campucana

text: Tropical rainforest

characteristic: habitat

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

characteristic: lifestage

text: Tithorea tarricina

text: THORAX

characteristic: organism part

characteristic: project name

text: Tithorea tarricina

text: FEMALE

text: N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: Colombia

text: Putumayo | Mocoa | Campucana

text: Tropical rainforest

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

text: Tithorea tarricina

text: LEG

characteristic: sample derived from

text: Tithorea tarricina

text: FEMALE

characteristic: sex

text: N

characteristic: symbiont

characteristic: tolid


text: National Institute of Biology

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:National Institute of Biology

characteristic: Submitter Id

text: Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better

characteristic: assembly quality

text: Unicycler

characteristic: assembly software

text: manual

characteristic: binning parameters

text: anvi-refine

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: anvi-summarize

characteristic: completeness software

characteristic: contamination score

text: MAG from mixed culture Mt009 (manually refined)

characteristic: description

text: coastal sea water

characteristic: environmental medium

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: marine environment

text: marine biome

characteristic: local environmental context

text: marine metagenome

characteristic: metagenomic source

text: Vibrio campbellii

characteristic: organism

text: Vibrio isolate

text: Vibrio campbellii

text: 16S gene

characteristic: taxonomic identity marker

text: Vibrio campbellii Mt009_b1

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: National Institute of Biology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: Unicycler

characteristic: assembly software

text: manual

characteristic: binning parameters

text: anvi-refine

text: aquatic biome

text: anvi-summarize

text: coastal sea water

text: Slovenia

text: marine environment

text: marine biome

text: marine metagenome

text: Enterovibrio norvegicus

text: Vibrio isolate

characteristic: project name

characteristic: sample derived from

text: Enterovibrio norvegicus

text: 16S gene

text: Enterovibrio norvegicus Mt009_b2


text: National Institute of Biology

text: public

text: Unicycler

text: manual

text: anvi-refine

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: completeness score

text: anvi-summarize

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: coastal sea water

characteristic: environmental medium

text: Slovenia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: marine environment

text: marine biome

characteristic: local environmental context

text: marine metagenome

characteristic: metagenomic source

text: Klebsiella pneumoniae

characteristic: organism

text: Vibrio isolate

text: Klebsiella pneumoniae

text: 16S gene

characteristic: taxonomic identity marker

text: Klebsiella pneumoniae Mt009_b3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSTITUT PASTEUR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INSTITUT PASTEUR

characteristic: Submitter Id

text: Cohnella sp. JJ-181

text: Cohnella sp. JJ-181

text: Whole genome sequencing of Cohnella sp. JJ-181 = CIP112018

characteristic: title


text: NTNU

text: public

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

characteristic: collection date

text: Gut sample, treated with Janthinobacterium sp.; EDM

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: fish metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NTNU

text: public

text: Salmo salar yolk sac fry

text: Skin sample, treated with Janthinobacterium sp.; EDM

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Fish skin

characteristic: local environmental context

text: fish metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: External Id

text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Salmo salar yolk sac fry

text: Water sample, treated with Janthinobacterium sp.; EDM

text: Fresh water

text: Norway

text: Water sample

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


text: NTNU

text: public

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

characteristic: collection date

text: Gut sample, Untreated; EDM

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

text: Salmo salar yolk sac fry

text: Skin sample, Untreated; EDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Fish skin

text: fish metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: fish metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

characteristic: INSDC center name

text: public

text: Salmo salar yolk sac fry

text: Water sample, Untreated; EDM

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Water sample

characteristic: local environmental context

text: fish metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


text: NTNU

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Gut sample, treated with Yersinia ruckeri; EDM

text: Fresh water

text: Norway

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

text: Skin sample, treated with Yersinia ruckeri; EDM

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Fish skin

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

text: Salmo salar yolk sac fry

text: Water sample, treated with Yersinia ruckeri; EDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Water sample

text: fish metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: fish metagenome

text: Illumina

characteristic: sequencing method


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Salmo salar yolk sac fry

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Fish gut

characteristic: local environmental context

text: freshwater metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Gut sample, treated with Janthinobacterium sp.; LDM

text: Fresh water

text: Norway

text: Fish gut

text: freshwater metagenome

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina

characteristic: title


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Salmo salar yolk sac fry

text: Skin sample, treated with Janthinobacterium sp.; LDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Fish skin

text: freshwater metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

characteristic: INSDC last update

text: public

text: Salmo salar yolk sac fry

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Fish skin

characteristic: local environmental context

text: fish metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Water sample, treated with Janthinobacterium sp.; LDM

text: Fresh water

text: Norway

text: Water sample

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Water sample

text: freshwater metagenome

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

text: Salmo salar yolk sac fry

text: Gut sample, Untreated; LDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: fish metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

characteristic: INSDC last update

text: public

text: Salmo salar yolk sac fry

text: Gut sample, Untreated; LDM

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Fish gut

characteristic: local environmental context

text: freshwater metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Skin sample, Untreated; LDM

text: Fresh water

text: Norway

text: Fish skin

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

text: Skin sample, Untreated; LDM

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Fish skin

text: freshwater metagenome

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

text: Salmo salar yolk sac fry

text: Water sample, Untreated; LDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Water sample

text: freshwater metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Salmo salar yolk sac fry

text: Water sample, Untreated; LDM

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Water sample

characteristic: local environmental context

text: fish metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Gut sample, treated with Yersinia ruckeri; LDM

text: Fresh water

text: Norway

text: Fish gut

text: freshwater metagenome

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Fish gut

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina

characteristic: title


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Salmo salar yolk sac fry

text: Skin sample, treated with Yersinia ruckeri; LDM

text: Fresh water

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Fish skin

text: freshwater metagenome

text: Source Microbiota Salmo salar

characteristic: project name

text: freshwater metagenome

text: Illumina

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: NTNU

characteristic: INSDC last update

text: public

text: Salmo salar yolk sac fry

text: Fresh water

text: Norway

characteristic: geographic location (longitude)

text: Fish skin

characteristic: local environmental context

text: fish metagenome

characteristic: organism

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NTNU

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Salmo salar yolk sac fry

characteristic: broad-scale environmental context

text: Water sample, treated with Yersinia ruckeri; LDM

text: Fresh water

text: Norway

text: Water sample

text: fish metagenome

text: Source Microbiota Salmo salar

text: fish metagenome

text: Illumina


text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Salmo salar yolk sac fry

characteristic: collection date

characteristic: description

text: Fresh water

characteristic: environmental medium

text: Norway

text: Water sample

text: freshwater metagenome

text: Source Microbiota Salmo salar

text: freshwater metagenome

text: Illumina

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:DKTK Clinical Cooperation Unit (CCU) Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: house mouse

characteristic: common name

text: Protocols: Mice were anesthetized and perfused with PBS. Brains of tumor-bearing mice were extracted and the tumor bearing hemisphere was cut into pieces and digested with 50 µg/ml liberase (Sigma) at 37°C for 30 minutes and subsequently mashed through a 100 µm and 70 µm strainer (Miltenyi). Myelin was removed using a 30% continuous Percoll (GE Healthcare) gradient and centrifugation at 2700 rpm. Immune cells were isolated as described above. Murine cells were blocked with rat anti-mouse CD16/32 (0.5 μg per well, eBioscience). Dextramer staining was performed according to manufacturer’s protocol (Immudex): after blocking, cells were incubated with 1:10 dextramer (PE and APC) dilution in 50 µl PBS for 10 minutes. Respective antibodies in PBS were added in 50 µl total volume and stained for 30 minutes. Following antibodies were used: CD45-BV510, CD3-FITC, MHCII-AF700, CD11b-PEDazzle, CD8-PercpCy5.5. eFluor 780 fixable viability dye (eBioscience) was used according to manufacturer's protocol to exclude dead cells. For scRNA-Seq, cells were pre-incubated for 10 minutes with titrated amounts of TotalSeq C hashing antibodies. Cells were sorted on a BDAria II and BD Aria Fusion through an 85 µM nozzle and 4-way purity. Cells were sorted in 20 µl 0.04% BSA in PBS and kept on ice until processing. RNA extraction was performed according to manufacturers protocol (10x genomics, Chromium Single Cell V(D)J Reagent Kits User Guide (v1.1) with Feature Barcoding technology for Cell Surface Protein) Library construction was performed according to manufacturers protocol (10x genomics, Chromium Single Cell V(D)J Reagent Kits User Guide (v1.1) with Feature Barcoding technology for Cell Surface Protein)

text: wild type genotype

characteristic: genotype

text: CD3 positive

characteristic: immunophenotype

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DKTK Clinical Cooperation Unit (CCU) Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: leukocyte

text: house mouse

text: wild type genotype

text: CD3 negative

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: leukocyte

text: house mouse

characteristic: description

text: wild type genotype

text: CD3 positive

text: Mus musculus

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male

characteristic: title


E-MTAB-12523:MHCII KO_CD3negative

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12523:MHCII KO_CD3negative

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: house mouse

characteristic: common name

text: Cx3CR1CreERT2-MHCII flox

characteristic: genotype

text: CD3 negative

characteristic: immunophenotype

text: Mus musculus

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male

text: MHCII KO_CD3negative


E-MTAB-12523:MHCII KO_CD3positive

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12523:MHCII KO_CD3positive

text: ArrayExpress

text: leukocyte

text: house mouse

text: Cx3CR1CreERT2-MHCII flox

text: CD3 positive

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: MHCII KO_CD3positive


E-MTAB-12523:MHCII KO_Dext+

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12523:MHCII KO_Dext+

characteristic: Submitter Id

text: ArrayExpress

text: leukocyte

text: house mouse

text: Cx3CR1CreERT2-MHCII flox

text: SIINFEKL-reactive

text: Mus musculus

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male

text: MHCII KO_Dext+


E-MTAB-12523:MHCII WT_CD3negative

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12523:MHCII WT_CD3negative

text: ArrayExpress

text: leukocyte

text: house mouse

characteristic: description

text: MHCII flox

text: CD3 negative

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male

text: MHCII WT_CD3negative


E-MTAB-12523:MHCII WT_CD3positive

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-12523:MHCII WT_CD3positive

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: house mouse

characteristic: common name

text: MHCII flox

characteristic: genotype

text: CD3 positive

text: Mus musculus

text: Mus musculus

text: brain

text: neoplasm

text: Mus musculus

text: male

text: MHCII WT_CD3positive

characteristic: title


E-MTAB-12523:MHCII WT_Dext+

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-12523:MHCII WT_Dext+

text: ArrayExpress

text: leukocyte

text: house mouse

text: MHCII flox

text: SIINFEKL-reactive

characteristic: immunophenotype

text: Mus musculus

text: Mus musculus

text: brain

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

text: MHCII WT_Dext+


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:292-1

tag: Namespace:UNIVERSITY OF PERPIGNAN/CNRS

characteristic: collection date

text: thale cress

text: 135 Mb

characteristic: estimated size

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Seeds were first germinated at 20 °C and after 4 to 7 days seedlings were either transferred to 27 °C under short day or at 37°C under long day condition. Heat treatments were done by transferring plants in pre-heated MLR-352 Plant Growth Chambers (PHCbi Sanyo)

characteristic: isolation and growth condition

text: Arabidopsis thaliana

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text: in vitro culture MS 1/2 0.5% plant agar

characteristic: plant growth medium

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characteristic: plant structure

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text: Arabidopsis thaliana


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text: 135 Mb

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text: Arabidopsis thaliana

characteristic: organism

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text: Arabidopsis thaliana

characteristic: title


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characteristic: INSDC last update

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text: ena-SAMPLE-TAB-16-01-2023-15:06:30:293-3

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characteristic: estimated size

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characteristic: geographic location (country and/or sea)

text: Arabidopsis thaliana

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text: Arabidopsis thaliana

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text: Arabidopsis thaliana


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characteristic: estimated size

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text: Arabidopsis thaliana


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characteristic: estimated size

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characteristic: geographic location (country and/or sea)

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text: UNIVERSITY OF PERPIGNAN/CNRS

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text: Arabidopsis thaliana

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characteristic: plant structure

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text: Arabidopsis thaliana


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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: Arabidopsis thaliana

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characteristic: ENA-CHECKLIST

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text: Arabidopsis thaliana

characteristic: organism

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana

characteristic: title


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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text: thale cress

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text: Arabidopsis thaliana

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text: in vitro culture MS 1/2 0.5% plant agar

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text: leaves

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text: UNIVERSITY OF PERPIGNAN/CNRS

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characteristic: collection date

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characteristic: common name

text: 135 Mb

characteristic: estimated size

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

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characteristic: plant structure

characteristic: ploidy

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

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text: UNIVERSITY OF PERPIGNAN/CNRS

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text: thale cress

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characteristic: geographic location (longitude)

characteristic: isolation and growth condition

text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:303-18

characteristic: Submitter Id

text: thale cress

text: 135 Mb

text: France

text: Seeds were first germinated at 20 °C and after 4 to 7 days seedlings were either transferred to 27 °C under short day or at 37°C under long day condition. Heat treatments were done by transferring plants in pre-heated MLR-352 Plant Growth Chambers (PHCbi Sanyo)

text: Arabidopsis thaliana

characteristic: organism

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana

characteristic: title


text: UNIVERSITY OF PERPIGNAN/CNRS

text: public

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characteristic: collection date

text: thale cress

characteristic: common name

text: 135 Mb

characteristic: estimated size

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Arabidopsis thaliana

characteristic: plant developmental stage

text: in vitro culture MS 1/2 0.5% plant agar

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text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

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text: public

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:303-20

text: thale cress

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text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

characteristic: plant structure

characteristic: ploidy

text: Arabidopsis thaliana


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:304-21

characteristic: Submitter Id

text: thale cress

text: 135 Mb

text: France

characteristic: geographic location (longitude)

characteristic: isolation and growth condition

text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana


text: UNIVERSITY OF PERPIGNAN/CNRS

text: public

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:304-22

characteristic: collection date

text: thale cress

characteristic: common name

text: 135 Mb

characteristic: estimated size

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Arabidopsis thaliana

characteristic: organism

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana

characteristic: title


characteristic: ENA-CHECKLIST

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text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:304-23

text: thale cress

text: 135 Mb

text: France

text: Arabidopsis thaliana

characteristic: plant developmental stage

text: in vitro culture MS 1/2 0.5% plant agar

characteristic: plant growth medium

text: leaves

text: Arabidopsis thaliana


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:304-24

characteristic: Submitter Id

text: thale cress

text: 135 Mb

text: France

text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

characteristic: plant structure

characteristic: ploidy

text: Arabidopsis thaliana


text: UNIVERSITY OF PERPIGNAN/CNRS

text: public

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:305-25

characteristic: collection date

text: thale cress

characteristic: common name

text: 135 Mb

characteristic: estimated size

text: France

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: isolation and growth condition

text: Arabidopsis thaliana

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:305-26

text: thale cress

text: 135 Mb

text: France

text: Arabidopsis thaliana

characteristic: organism

text: in vitro culture MS 1/2 0.5% plant agar

text: leaves

text: Arabidopsis thaliana

characteristic: title


characteristic: External Id

text: UNIVERSITY OF PERPIGNAN/CNRS

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-15:06:30:305-27

characteristic: Submitter Id

text: thale cress

text: 135 Mb

text: France

text: Arabidopsis thaliana

characteristic: plant developmental stage

text: in vitro culture MS 1/2 0.5% plant agar

characteristic: plant growth medium

text: leaves

text: Arabidopsis thaliana


text: UNIVERSITY OF COPENHAGEN

text: public

tag: Namespace:UNIVERSITY OF COPENHAGEN

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647697 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus crispatus

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Lactobacillus crispatus

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647697_bin.2_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647699 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Candidatus Lactobacillus pullistercoris

characteristic: organism

text: Candidatus Lactobacillus pullistercoris

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Candidatus Lactobacillus pullistercoris

text: multi-marker approach

text: Binned metagenome: ERR4647699_bin.1_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Limosilactobacillus reuteri

characteristic: project name

characteristic: sample derived from

text: Limosilactobacillus reuteri

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus reuteri

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647697_bin.1_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647693 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Lactobacillus crispatus

characteristic: organism

text: Lactobacillus crispatus

text: multi-marker approach

text: Binned metagenome: ERR4647693_bin.2_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647695 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

characteristic: project name

characteristic: sample derived from

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__;c__;o__;f__;g__Candidatus Galligastranaerophilus;s__Candidatus Galligastranaerophilus faecipullorum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647695_bin.10_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Lactobacillus crispatus

characteristic: organism

text: Lactobacillus crispatus

text: multi-marker approach

text: Binned metagenome: ERR4647695_bin.9_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic runs ERR4647691,ERR4647692,ERR4647693,ERR4647694,ERR4647695,ERR4647696,ERR4647697,ERR4647698,ERR4647699,ERR4647712,ERR4647713,ERR4647716 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Eubacteriales bacterium

characteristic: project name

text: SAMEA7368185,SAMEA7368180,SAMEA7368178,SAMEA7368184,SAMEA7368182,SAMEA7368179,SAMEA7368183,SAMEA7368186,SAMEA7368188,SAMEA7368177,SAMEA7368181,SAMEA7368187

characteristic: sample derived from

text: uncultured Eubacteriales bacterium

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647all_bin.18_MetaWRAP_v1.1_bin


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: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus salivarius

characteristic: organism

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

text: Ligilactobacillus salivarius

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus salivarius

text: multi-marker approach

text: Binned metagenome: ERR4647all_bin.13_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647697 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus johnsonii

characteristic: project name

characteristic: sample derived from

text: Lactobacillus johnsonii

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus johnsonii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647697_bin.3_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647716 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Romboutsia sp.

characteristic: organism

text: uncultured Romboutsia sp.

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Peptostreptococcaceae;g__Romboutsia;s__

text: multi-marker approach

text: Binned metagenome: ERR4647716_bin.17_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647695 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Bacilli bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Bacilli bacterium

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__;f__;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647695_bin.7_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Candidatus Helicobacter avistercoris

characteristic: organism

text: Candidatus Helicobacter avistercoris

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__Candidatus Helicobacter avistercoris

text: multi-marker approach

text: Binned metagenome: ERR4647716_bin.12_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic runs ERR4647691,ERR4647692,ERR4647693,ERR4647694,ERR4647695,ERR4647696,ERR4647697,ERR4647698,ERR4647699,ERR4647712,ERR4647713,ERR4647716 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Candidatus Helicobacter avistercoris

characteristic: project name

text: SAMEA7368185,SAMEA7368180,SAMEA7368178,SAMEA7368184,SAMEA7368182,SAMEA7368179,SAMEA7368183,SAMEA7368186,SAMEA7368188,SAMEA7368177,SAMEA7368181,SAMEA7368187

characteristic: sample derived from

text: Candidatus Helicobacter avistercoris

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647all_bin.33_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

characteristic: organism

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__Faecalibacterium;s__Candidatus Faecalibacterium faecigallinarum

text: multi-marker approach

text: Binned metagenome: ERR4647695_bin.8_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Limosilactobacillus oris

characteristic: project name

characteristic: sample derived from

text: Limosilactobacillus oris

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus oris

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647all_bin.3_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647716 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Corynebacterium stationis

characteristic: organism

text: Corynebacterium stationis

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__Corynebacterium stationis

text: multi-marker approach

text: Binned metagenome: ERR4647716_bin.1_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Lactobacillus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Lactobacillus sp.

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647716_bin.3_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647698 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Limosilactobacillus vaginalis

characteristic: organism

text: Limosilactobacillus vaginalis

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus vaginalis

text: multi-marker approach

text: Binned metagenome: ERR4647698_bin.4_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR5100007 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Ligilactobacillus aviarius

characteristic: project name

characteristic: sample derived from

text: Ligilactobacillus aviarius

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus aviarius

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR5100007_bin.4_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Lactobacillaceae bacterium

characteristic: organism

text: uncultured Lactobacillaceae bacterium

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__;s__

text: multi-marker approach

text: Binned metagenome: ERR4647716_bin.9_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647699 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Enterococcus sp.

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: uncultured Enterococcus sp.

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647699_bin.6_MetaWRAP_v1.1_bin


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: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic runs ERR4647691,ERR4647692,ERR4647693,ERR4647694,ERR4647695,ERR4647696,ERR4647697,ERR4647698,ERR4647699,ERR4647712,ERR4647713,ERR4647716 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Oscillospiraceae bacterium

characteristic: organism

text: SAMEA7368185,SAMEA7368180,SAMEA7368178,SAMEA7368184,SAMEA7368182,SAMEA7368179,SAMEA7368183,SAMEA7368186,SAMEA7368188,SAMEA7368177,SAMEA7368181,SAMEA7368187

text: uncultured Oscillospiraceae bacterium

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__;s__

text: multi-marker approach

text: Binned metagenome: ERR4647all_bin.19_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647713 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Corynebacterium stationis

characteristic: project name

characteristic: sample derived from

text: Corynebacterium stationis

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Corynebacteriaceae;g__Corynebacterium;s__Corynebacterium stationis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647713_bin.10_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus salivarius

characteristic: organism

text: Ligilactobacillus salivarius

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus salivarius

text: multi-marker approach

text: Binned metagenome: ERR4647699_bin.4_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Enteractinococcus sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Enteractinococcus sp.

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Micrococcales;f__Micrococcaceae;g__Enteractinococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647all_bin.32_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR5100006 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus salivarius

characteristic: organism

text: Ligilactobacillus salivarius

text: multi-marker approach

text: Binned metagenome: ERR5100006_bin.2_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647716 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Enterococcus faecium

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Enterococcus faecium

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__Enterococcus faecium

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647716_bin.2_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR5100007 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Lactobacillus crispatus

characteristic: organism

text: Lactobacillus crispatus

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus

text: multi-marker approach

text: Binned metagenome: ERR5100007_bin.2_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647698 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Campylobacter jejuni

characteristic: project name

characteristic: sample derived from

text: Campylobacter jejuni

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter;s__Campylobacter jejuni

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647698_bin.1_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

characteristic: organism

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Candidatus Limosilactobacillus excrementigallinarum

text: multi-marker approach

text: Binned metagenome: ERR4647716_bin.20_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic runs ERR4647691,ERR4647692,ERR4647693,ERR4647694,ERR4647695,ERR4647696,ERR4647697,ERR4647698,ERR4647699,ERR4647712,ERR4647713,ERR4647716 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Lactobacillaceae bacterium

characteristic: project name

text: SAMEA7368185,SAMEA7368180,SAMEA7368178,SAMEA7368184,SAMEA7368182,SAMEA7368179,SAMEA7368183,SAMEA7368186,SAMEA7368188,SAMEA7368177,SAMEA7368181,SAMEA7368187

characteristic: sample derived from

text: uncultured Lactobacillaceae bacterium

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647all_bin.10_MetaWRAP_v1.1_bin


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: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: not provided

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic runs ERR4647692,ERR4647693,ERR4647713 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus salivarius

characteristic: organism

text: Ligilactobacillus salivarius

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus salivarius

text: multi-marker approach

text: Binned metagenome: ERR4647lq_bin.6_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR5100006 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Escherichia coli

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken caecum and ileum samples. Samples selected for this batch were randomised among trials (feed), age, and breed to overcome batch effect. The caecum samples in this project contributed to the chicken caecum MAG catalogue (project: PRJEB55374 [ERP140263]), and the ileum samples contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Escherichia coli

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR5100006_bin.3_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647694 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Eubacteriales bacterium

characteristic: organism

text: uncultured Eubacteriales bacterium

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__;g__;s__

text: multi-marker approach

text: Binned metagenome: ERR4647694_bin.2_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647695 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Bacteroides fragilis

characteristic: project name

characteristic: sample derived from

text: Bacteroides fragilis

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides fragilis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647695_bin.4_MetaWRAP_v1.1_bin


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

text: metaSPAdes v3.14.1

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647699 of study ERP122587.

text: Ileum

text: Spain

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Dietzia sp.

characteristic: organism

text: uncultured Dietzia sp.

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinomycetia;o__Corynebacteriales;f__Dietziaceae;g__Dietzia;s__

text: multi-marker approach

text: Binned metagenome: ERR4647699_bin.10_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: metaSPAdes v3.14.1

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR4647698 of study ERP122587.

characteristic: description

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Candidatus Helicobacter avistercoris

characteristic: project name

characteristic: sample derived from

text: Candidatus Helicobacter avistercoris

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Epsilonproteobacteria;o__Campylobacterales;f__Helicobacteraceae;g__Helicobacter;s__Candidatus Helicobacter avistercoris

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR4647698_bin.3_MetaWRAP_v1.1_bin