characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnoclostridium sp.

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnoclostridium sp.

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__[Clostridium] bolteae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753921_bin.12_metawrap_v1.3_MAG

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

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 v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753921 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Eggerthella lenta

text: Two consortia of human commensal bacteria, rationally designed around functionalities that are underrepresented in the gut microbiome of IBD patients, robustly corrected colitis-related microbial dysbiosis, dysregulated metabolism and treated T cell-mediated colitis.

text: Eggerthella lenta

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Eggerthella;s__Eggerthella lenta

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753921_bin.13_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Flavonifractor plautii

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: Flavonifractor plautii

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Flavonifractor;s__Flavonifractor plautii

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753921_bin.2_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Holdemania filiformis

text: Holdemania filiformis

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemania;s__Holdemania filiformis

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753921_bin.5_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753922 of study SRP307210.

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Eisenbergiella massiliensis

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: Eisenbergiella massiliensis

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Eisenbergiella;s__Eisenbergiella massiliensis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753922_bin.1_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: [Clostridium] innocuum

text: [Clostridium] innocuum

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Erysipelatoclostridium;s__[Clostridium] innocuum

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753922_bin.13_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: [Clostridium] symbiosum

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: [Clostridium] symbiosum

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__[Clostridium] symbiosum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753922_bin.2_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

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 v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Enterococcus faecium

text: Enterococcus faecium

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome 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

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753922_bin.4_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Clostridia bacterium

characteristic: organism

text: Two consortia of human commensal bacteria, rationally designed around functionalities that are underrepresented in the gut microbiome of IBD patients, robustly corrected colitis-related microbial dysbiosis, dysregulated metabolism and treated T cell-mediated colitis.

characteristic: project name

characteristic: sample derived from

text: uncultured Clostridia bacterium

text: Illumina HiSeq 4000

characteristic: sequencing method

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

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753922_bin.9_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753923 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Butyricicoccus sp.

text: uncultured Butyricicoccus sp.

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Butyricicoccus;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753923_bin.1_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Lachnoclostridium sp.

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnoclostridium sp.

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__[Clostridium] aldenense

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753923_bin.8_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753928 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Butyricicoccus sp.

text: uncultured Butyricicoccus sp.

text: Illumina HiSeq 4000

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753928_bin.1_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753929 of study SRP307210.

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Murimonas intestini

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: Murimonas intestini

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Murimonas;s__Murimonas intestini

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753929_bin.1_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Bacteroides eggerthii

text: Bacteroides eggerthii

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome 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 eggerthii

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753929_bin.10_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

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

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Ruminococcus sp.

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Ruminococcus sp.

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Ruminococcaceae;g__Ruminococcus;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753929_bin.11_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Parabacteroides distasonis

text: Two consortia of human commensal bacteria, rationally designed around functionalities that are underrepresented in the gut microbiome of IBD patients, robustly corrected colitis-related microbial dysbiosis, dysregulated metabolism and treated T cell-mediated colitis.

text: Parabacteroides distasonis

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides;s__Parabacteroides distasonis

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753929_bin.12_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Turicibacter sp.

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Turicibacter sp.

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Turicibacter;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753929_bin.2_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Clostridia bacterium

text: uncultured Clostridia bacterium

text: Illumina HiSeq 4000

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

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753929_bin.5_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Sutterellaceae bacterium

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Sutterellaceae bacterium

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Sutterellaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753929_bin.7_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753932 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Lachnoclostridium sp.

text: uncultured Lachnoclostridium sp.

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Lachnoclostridium;s__[Clostridium] asparagiforme

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753932_bin.8_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753933 of study SRP307210.

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Gordonibacter pamelaeae

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: Gordonibacter pamelaeae

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Eggerthellales;f__Eggerthellaceae;g__Gordonibacter;s__Gordonibacter pamelaeae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753933_bin.1_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

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 v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753937 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Alistipes sp.

text: uncultured Alistipes sp.

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753937_bin.1_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Bacteroides uniformis

characteristic: organism

text: Two consortia of human commensal bacteria, rationally designed around functionalities that are underrepresented in the gut microbiome of IBD patients, robustly corrected colitis-related microbial dysbiosis, dysregulated metabolism and treated T cell-mediated colitis.

characteristic: project name

characteristic: sample derived from

text: Bacteroides uniformis

text: Illumina HiSeq 4000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome 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 uniformis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753937_bin.11_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Collinsella sp.

text: uncultured Collinsella sp.

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753937_bin.3_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: not provided

text: metawrap v1.3

text: mouse digestive system

text: EBI-EMG

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Alistipes sp.

characteristic: organism

characteristic: project name

characteristic: sample derived from

text: uncultured Alistipes sp.

text: Illumina HiSeq 4000

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR13753937_bin.9_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

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: not provided

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR13753940 of study SRP307210.

text: feces

text: USA

characteristic: geographic location (country and/or sea)

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: Alistipes finegoldii

text: Alistipes finegoldii

text: Illumina HiSeq 4000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__Alistipes finegoldii

text: multi-marker approach

text: Metagenome-assembled genome: SRR13753940_bin.5_metawrap_v1.3_MAG


text: Kathrine Stene-Johansen, Kamilla Heddeland Instefjord, Hilde Elshaug, Garcia Llorente Ignacio, Jon Bråte, Engebretsen Serina Beate, Pedersen Benedikte Nevjen, Line Victoria Moen, Hilde Nordby Falkenhaug, Debech Nadia, Atiya R Ali, Marie Paulsen Madsen, Rasmus Riis Kopperud, Hilde Vollan, Karoline Bragstad, Olav Hungnes

characteristic: Authors

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

tag: Namespace:Norwegian Institute of Public Health (NIPH)

text: ELIXIR-Norway

text: Department of Medical Microbiology - section Molde, Molde Hospital ; Parkveien 84, N-6407 Molde, Norway

characteristic: collecting institution

text: not provided

characteristic: collector name

text: Norway

text: More og Romsdal

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: title


characteristic: Authors

characteristic: External Id

text: Norwegian Institute of Public Health (NIPH)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: Department Medical Microbiology, Baerum Hospital, Vestre Viken Health Trust ; P.O.Box 800, N-3004 Drammen, Norway

characteristic: collection date

text: not provided

text: Norway

characteristic: geographic location (country and/or sea)

text: Viken

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

text: ELIXIR-Norway

characteristic: collecting institution

text: not provided

characteristic: collector name

text: Norway

text: More og Romsdal

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

text: Haugesund Hospital, laboratory for Medical Microbiology ; P.O.Box 2170, N-5504 Haugesund, Norway

text: not provided

text: Norway

text: Rogaland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: Hospital of Southern Norway - Kristiansand, Department of Medical Microbiology ; P.O.Box 416 Lundsiden, N-4604 Kristiansand, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Agder

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

text: Haukeland University Hospital, Dept. of Microbiology ; P.O.Box 1400, N-5021 Bergen, Norway

text: not provided

text: Norway

text: Vestland

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Furst Medical Laboratory ; Soeren Bulls vei 25, N-1051 Oslo, Norway

text: not provided

text: Norway

text: Oslo

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

characteristic: broker name

text: Medical Microbiology Unit, Department for Laboratory Medicine, Drammen Hospital, Vestre Viken Health Trust ; P.O.Box 800, N-3004 Drammen, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Viken

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Innlandet Hospital Trust, Division Lillehammer, Department for Medical Microbiology ; P.O.Box 990, N-2629 Lillehammer, Norway

text: not provided

text: Norway

text: Innlandet

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

text: Ostfold Hospital Trust - Kalnes, Centre for Laboratory Medicine, Section for gene technology and infection serology ; P.O.Box 300, N-1714 Graalum, Norway

text: not provided

text: Norway

text: Viken

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: Foerde Hospital, Department of Microbiology ; P.O.Box 1000, N-6807 Foerde, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Vestland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

text: Department of Medical Microbiology, St. Olavs hospital ; P.O.box 3250 Torgarden, N-7006 Trondheim, Norway

text: not provided

text: Norway

text: Trondelag

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Vestfold Hospital, Toensberg, Department of Microbiology ; P.O.Box 2168, N-3103 Toensberg, Norway

text: not provided

text: Norway

text: Vestfold og Telemark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

characteristic: broker name

text: University Hospital of Northern Norway, Department for Microbiology and Infectious Disease Control ; P.O.Box 56, N-9038 Tromsoe, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Nordland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: GISAID Accession ID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Telemark Hospital Trust - Skien, Dept. of Medical Microbiology ; P.O.Box 2900 Kjørbekk, N-3710 Skien

text: not provided

text: Norway

text: Vestfold og Telemark

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

text: not provided


text: Kathrine Stene-Johansen, Kamilla Heddeland Instefjord, Hilde Elshaug, Garcia Llorente Ignacio, Jon Bråte, Engebretsen Serina Beate, Pedersen Benedikte Nevjen, Line Victoria Moen, Hilde Nordby Falkenhaug, Debech Nadia, Atiya R Ali, Marie Paulsen Madsen, Rasmus Riis Kopperud, Hilde Vollan, Karoline Bragstad, Olav Hungnes

characteristic: Authors

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

text: Nordland Hospital - Bodo, Laboratory Department, Molecular Biology Unit ; P.O.Box 1480, N-8092 Bodo, Norway

text: not provided

text: Norway

text: Nordland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

tag: Namespace:Laboratory of Genomics and Bioinformatics, Comenius University Science Park

characteristic: Submitter Id

text: Science Park of Comenius University of Bratislava

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

characteristic: common name

text: Slovakia

characteristic: geographic location (country and/or sea)

unit: year

characteristic: host age

text: Human

text: not provided

text: Homo sapiens

text: male

text: RNA

text: Nasopharyngeal swab

characteristic: isolation source-host associated

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status


characteristic: External Id

text: Laboratory of Genomics and Bioinformatics, Comenius University Science Park

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: not provided

text: Slovakia

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: RNA

characteristic: isolate

text: Nasopharyngeal swab


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

text: not provided

text: Slovakia

text: Human

text: not provided

text: Homo sapiens

text: male

text: RNA

text: Nasopharyngeal swab

characteristic: organism


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: not provided

characteristic: collector name

characteristic: common name

text: Slovakia

characteristic: geographic location (country and/or sea)

characteristic: host age

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: RNA

text: Nasopharyngeal swab

characteristic: isolation source-host associated

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: SIB

text: EHNV, CH-1400 Yverdon, Switzerland

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/VD-CHUV-GEN13381/2022

characteristic: isolate

text: active surveillance not initiated by an outbreak

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: Hôpital Cantonal de Fribourg - HFR, CH-1752 Villars-sur-Glâne, Switzerland

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN14047/2022

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

text: EHNV, CH-1400 Yverdon, Switzerland

text: Switzerland

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13320/2022

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

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text: hCoV-19/Switzerland/VD-CHUV-GEN14048/2022

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text: hCoV-19/Switzerland/VD-CHUV-GEN14050/2022

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text: hCoV-19/Switzerland/VD-CHUV-GEN13353/2022

text: Severe acute respiratory syndrome coronavirus 2

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text: hCoV-19/Switzerland/VD-CHUV-GEN13363/2022

text: active surveillance in response to outbreak

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text: CHUV, CH-1011 Lausanne, Switzerland

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

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text: hCoV-19/Switzerland/VD-CHUV-GEN13309/2022

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text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

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text: Human

text: restricted access

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN12176/2022

characteristic: organism

text: active surveillance not initiated by an outbreak


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text: EHNV, CH-1400 Yverdon, Switzerland

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text: hCoV-19/Switzerland/VD-CHUV-GEN13325/2022

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text: public

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text: Hôpital ophtalmique Jules-Gonin, CH-1004 Lausanne, Switzerland

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN13375/2022

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text: CHUV, CH-1011 Lausanne, Switzerland

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text: Human

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text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13377/2022

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text: Hôpital Cantonal de Fribourg - HFR, CH-1752 Villars-sur-Glâne, Switzerland

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text: VD

text: Human

text: restricted access

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN13371/2022

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text: EHC MORGES, CH-1110 Morges, Switzerland

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text: hCoV-19/Switzerland/VD-CHUV-GEN13310/2022

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tag: Namespace:Wallenberg Centre for Molecular Medicine, Linkoping University, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences; Linkoping University, Sweden

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: HEK293T cells were harvested using TrypLE (Cat. #12604013, Gibco). Tissues were dissociated to single-cell via incubation in Tryple Express Enzyme (12-604-013, Thermo Fisher Scientific; 1 ml /4 limbs) for 15 minutes at 37C °C on a shaker. The cell suspension was resuspended in ice-cold PBS, filtered through a 40 m cell strainer (KKE3.1, Carl Roth) and further processed for CUT&RUN. Human embryonic kidney 293T cells (HEK293T) were cultured at 37 °C in a humidified incubator with 5% CO2. Cells were cultured in high glucose Dulbecco’s Modified Eagle Medium (Cat. #41965039, Gibco) supplemented with 10 % bovine calf serum (Cat. #1233C, Sigma-Aldrich) and 1X Penicillin-Streptomycin (Cat. #15140148, Gibco). HEK293T cells were cultured in media containing 10 µM CHIR99021 (Cat. #SML1046, Sigma Aldrich), LGK, or no stimulation. Samples were washed twice in wash buffer (HEPES pH 7.5 [20 mM], NaCl [150 mM], Spermidine [0.5 mM], Roche Complete Protease Inhibitor EDTA-Free (Cat. # COEDTAFRO, Roche)) and bound to 20 µl Magnetic ConA Agarose beads (Cat. #ABIN6952467, antibodies-online) equilibrated in binding buffer (HEPES pH 7.5 [20 mM], KCl [10 mM], CaCl2 [1 mM], MnCl2 [1 mM]). Antibody incubation was performed in 150 µl antibody buffer (wash buffer with digitonin [0.01%] and EDTA [2 mM]) with 1.5 µl anti-β-catenin antibody (Cat. #ABIN2855042, antibodies-online) overnight at 4 °C. Thereafter washes were performed with wash buffer containing 0.01% digitonin. After overnight incubation, samples were washed three times and pAG-MN protein was added at 0.6 µg/ml, in total volume of 150 µl. pAG/MNase was a gift from Steven Henikoff (Addgene plasmid #123461; http://n2t.net/addgene:123461; RRID: Addgene_123461), expressed and purified as described in (REF Meers 2019a). Samples were washed three times, followed by digestion for 30 min in wet ice in wash buffer supplemented with 2 mM CaCl2. 2X stop buffer (NaCl [340 mM], EDTA [20 mM], EGTA [4 mM], digitonin [0.05%], RNase A [100 µg/ml], glycogen [50 µl/ml]) was added to stop the reaction, and samples were incubated for 30 min at 37 °C. Beads were collected on the magnet and liquid transferred to a new tube. 2.5 µl proteinase K (Cat. #P8107S, New England BioLabs) and 2 µl 10% SDS were added, and samples incubated for 1 hr at 50 °C. Cells were washed three times in Nuclear Extraction (NE) buffer (HEPES-KOH pH-8.2 [20 mM], KCl [10 mM], Spermidine [0.5 mM], IGEPAL [0.05%], Glycerol [20%], Roche Complete Protease Inhibitor EDTA-Free), resuspended in 40 µl NE per sample and bound to 20 µl Magnetic ConA Agarose beads equilibrated in binding buffer. After incubation nuclei and beads are resuspended for 5 min in EDTA wash buffer (wash buffer with EDTA [0.2 mM]). Samples were divided in 200 µl PCR tubes and antibody incubation was performed in 200 µl wash buffer with 2 µl of antibody (for antibody and batch information, see Table 1) ON at 4 °C on a rotator. After ON incubation samples were washed 5 times in wash buffer and resuspended in 200 µl of pAG-MN buffer (wash buffer with pAG-MN 0.6 µg/ml) for 30 min at 4 °C on a rotator. Samples were washed five times, followed by digestion for 30 min in wet ice in wash buffer with 2 mM CaCl2. After 30 min the digestion buffer was removed and the reaction was stopped with 50 µl of 1X Urea STOP buffer (NaCl [100 mM], EDTA [2 mM], EGTA [2 mM], IGEPAL [0.5%], Urea [8.8 M]) and the samples were incubated 1 hr at 4°C. Beads were collected on the magnet and liquid transferred to a new PCR tube in which it was cleaned up twice using Mag-Bind TotalPure NGS beads (Cat. #M1327, Omega Bio-Tek) at 2X, and then resuspended in 20 µl Tris-HCl pH 7.5. Library preparation was performed using the KAPA Hyper Prep Kit for Illumina platforms (Cat. #KK8504, KAPA Biosystems) according to the manufacturer’s guidelines with the following modifications. End repair and A-tailing was performed with 0.4X volume reactions with 20 µl of purified DNA. The thermocycler conditions were set to 12 °C for 15 min, 37 °C for 15 min and 58 °C for 25 min to prevent thermal degradation of the shortest fragments. Adapter ligation was performed in 0.4X volume reactions. KAPA Dual Indexed adapters were used at 0.15 µM. A post-ligation clean-up was performed with Mag-Bind TotalPure NGS beads at 1.2X the sample volume. Resuspension was done in 10 mM Tris-HCl pH 8.0. Library amplification was performed in 0.5X volume reactions. The cycling conditions were set as follows: 45 sec initial denaturation at 98 °C, 15 sec denaturation at 98 °C, 10 sec annealing/elongation at 60 °C, 1 min final extension at 72 °C, hold at 4 °C, with 13 cycles. After amplification, a post-amplification cleanup was performed using NGS beads at 1.2X sample volume. Libraries were then run on an E-Gel EX 2% agarose gel (Cat. # G402022, Invitrogen) for 10 min using the E-Gel Power Snap Electrophoresis System (Invitrogen). Bands of interest between 150 and 500 bp were excised and purified using the GeneJET Gel Extraction Kit (Cat. #K0691, Thermo Scientific) according to manufacturer’s instructions.

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wallenberg Centre for Molecular Medicine, Linkoping University, Sweden; Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology; Faculty of Medicine and Health Sciences; Linkoping University, Sweden

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: HEK293T cells were harvested using TrypLE (Cat. #12604013, Gibco). Tissues were dissociated to single-cell via incubation in Tryple Express Enzyme (12-604-013, Thermo Fisher Scientific; 1 ml /4 limbs) for 15 minutes at 37C °C on a shaker. The cell suspension was resuspended in ice-cold PBS, filtered through a 40 m cell strainer (KKE3.1, Carl Roth) and further processed for CUT&RUN. The age of embryos was determined according to timed mating and vaginal plug observation (E0.5 dpc) and confirmed by morphological criteria. Pregnant females were sacrificed by cervical dislocation and E11.5 embryos were surgically removed. Tissues were dissected under a dissection stereomicroscope (SZ61, Olympus). Samples were washed twice in wash buffer (HEPES pH 7.5 [20 mM], NaCl [150 mM], Spermidine [0.5 mM], Roche Complete Protease Inhibitor EDTA-Free (Cat. # COEDTAFRO, Roche)) and bound to 20 µl Magnetic ConA Agarose beads (Cat. #ABIN6952467, antibodies-online) equilibrated in binding buffer (HEPES pH 7.5 [20 mM], KCl [10 mM], CaCl2 [1 mM], MnCl2 [1 mM]). Antibody incubation was performed in 150 µl antibody buffer (wash buffer with digitonin [0.01%] and EDTA [2 mM]) with 1.5 µl anti-β-catenin antibody (Cat. #ABIN2855042, antibodies-online) overnight at 4 °C. Thereafter washes were performed with wash buffer containing 0.01% digitonin. After overnight incubation, samples were washed three times and pAG-MN protein was added at 0.6 µg/ml, in total volume of 150 µl. pAG/MNase was a gift from Steven Henikoff (Addgene plasmid #123461; http://n2t.net/addgene:123461; RRID: Addgene_123461), expressed and purified as described in (REF Meers 2019a). Samples were washed three times, followed by digestion for 30 min in wet ice in wash buffer supplemented with 2 mM CaCl2. 2X stop buffer (NaCl [340 mM], EDTA [20 mM], EGTA [4 mM], digitonin [0.05%], RNase A [100 µg/ml], glycogen [50 µl/ml]) was added to stop the reaction, and samples were incubated for 30 min at 37 °C. Beads were collected on the magnet and liquid transferred to a new tube. 2.5 µl proteinase K (Cat. #P8107S, New England BioLabs) and 2 µl 10% SDS were added, and samples incubated for 1 hr at 50 °C. Library preparation was performed using the KAPA Hyper Prep Kit for Illumina platforms (Cat. #KK8504, KAPA Biosystems) according to the manufacturer’s guidelines with the following modifications. End repair and A-tailing was performed with 0.4X volume reactions with 20 µl of purified DNA. The thermocycler conditions were set to 12 °C for 15 min, 37 °C for 15 min and 58 °C for 25 min to prevent thermal degradation of the shortest fragments. Adapter ligation was performed in 0.4X volume reactions. KAPA Dual Indexed adapters were used at 0.15 µM. A post-ligation clean-up was performed with Mag-Bind TotalPure NGS beads at 1.2X the sample volume. Resuspension was done in 10 mM Tris-HCl pH 8.0. Library amplification was performed in 0.5X volume reactions. The cycling conditions were set as follows: 45 sec initial denaturation at 98 °C, 15 sec denaturation at 98 °C, 10 sec annealing/elongation at 60 °C, 1 min final extension at 72 °C, hold at 4 °C, with 13 cycles. After amplification, a post-amplification cleanup was performed using NGS beads at 1.2X sample volume. Libraries were then run on an E-Gel EX 2% agarose gel (Cat. # G402022, Invitrogen) for 10 min using the E-Gel Power Snap Electrophoresis System (Invitrogen). Bands of interest between 150 and 500 bp were excised and purified using the GeneJET Gel Extraction Kit (Cat. #K0691, Thermo Scientific) according to manufacturer’s instructions. Cells were washed three times in Nuclear Extraction (NE) buffer (HEPES-KOH pH-8.2 [20 mM], KCl [10 mM], Spermidine [0.5 mM], IGEPAL [0.05%], Glycerol [20%], Roche Complete Protease Inhibitor EDTA-Free), resuspended in 40 µl NE per sample and bound to 20 µl Magnetic ConA Agarose beads equilibrated in binding buffer. After incubation nuclei and beads are resuspended for 5 min in EDTA wash buffer (wash buffer with EDTA [0.2 mM]). Samples were divided in 200 µl PCR tubes and antibody incubation was performed in 200 µl wash buffer with 2 µl of antibody (for antibody and batch information, see Table 1) ON at 4 °C on a rotator. After ON incubation samples were washed 5 times in wash buffer and resuspended in 200 µl of pAG-MN buffer (wash buffer with pAG-MN 0.6 µg/ml) for 30 min at 4 °C on a rotator. Samples were washed five times, followed by digestion for 30 min in wet ice in wash buffer with 2 mM CaCl2. After 30 min the digestion buffer was removed and the reaction was stopped with 50 µl of 1X Urea STOP buffer (NaCl [100 mM], EDTA [2 mM], EGTA [2 mM], IGEPAL [0.5%], Urea [8.8 M]) and the samples were incubated 1 hr at 4°C. Beads were collected on the magnet and liquid transferred to a new PCR tube in which it was cleaned up twice using Mag-Bind TotalPure NGS beads (Cat. #M1327, Omega Bio-Tek) at 2X, and then resuspended in 20 µl Tris-HCl pH 7.5. Library preparation was performed using the KAPA Hyper Prep Kit for Illumina platforms (Cat. #KK8504, KAPA Biosystems) according to the manufacturer’s guidelines with the following modifications. End repair and A-tailing was performed with 0.4X volume reactions with 20 µl of purified DNA. The thermocycler conditions were set to 12 °C for 15 min, 37 °C for 15 min and 58 °C for 25 min to prevent thermal degradation of the shortest fragments. Adapter ligation was performed in 0.4X volume reactions. KAPA Dual Indexed adapters were used at 0.15 µM. A post-ligation clean-up was performed with Mag-Bind TotalPure NGS beads at 1.2X the sample volume. Resuspension was done in 10 mM Tris-HCl pH 8.0. Library amplification was performed in 0.5X volume reactions. The cycling conditions were set as follows: 45 sec initial denaturation at 98 °C, 15 sec denaturation at 98 °C, 10 sec annealing/elongation at 60 °C, 1 min final extension at 72 °C, hold at 4 °C, with 13 cycles. After amplification, a post-amplification cleanup was performed using NGS beads at 1.2X sample volume. Libraries were then run on an E-Gel EX 2% agarose gel (Cat. # G402022, Invitrogen) for 10 min using the E-Gel Power Snap Electrophoresis System (Invitrogen). Bands of interest between 150 and 500 bp were excised and purified using the GeneJET Gel Extraction Kit (Cat. #K0691, Thermo Scientific) according to manufacturer’s instructions.

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: forelimb

text: Mus musculus

text: JAX SWISS 034608

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: HEK293T cells were harvested using TrypLE (Cat. #12604013, Gibco). Tissues were dissociated to single-cell via incubation in Tryple Express Enzyme (12-604-013, Thermo Fisher Scientific; 1 ml /4 limbs) for 15 minutes at 37C °C on a shaker. The cell suspension was resuspended in ice-cold PBS, filtered through a 40 m cell strainer (KKE3.1, Carl Roth) and further processed for CUT&RUN. The age of embryos was determined according to timed mating and vaginal plug observation (E0.5 dpc) and confirmed by morphological criteria. Pregnant females were sacrificed by cervical dislocation and E11.5 embryos were surgically removed. Tissues were dissected under a dissection stereomicroscope (SZ61, Olympus). Samples were washed twice in wash buffer (HEPES pH 7.5 [20 mM], NaCl [150 mM], Spermidine [0.5 mM], Roche Complete Protease Inhibitor EDTA-Free (Cat. # COEDTAFRO, Roche)) and bound to 20 µl Magnetic ConA Agarose beads (Cat. #ABIN6952467, antibodies-online) equilibrated in binding buffer (HEPES pH 7.5 [20 mM], KCl [10 mM], CaCl2 [1 mM], MnCl2 [1 mM]). Antibody incubation was performed in 150 µl antibody buffer (wash buffer with digitonin [0.01%] and EDTA [2 mM]) with 1.5 µl anti-β-catenin antibody (Cat. #ABIN2855042, antibodies-online) overnight at 4 °C. Thereafter washes were performed with wash buffer containing 0.01% digitonin. After overnight incubation, samples were washed three times and pAG-MN protein was added at 0.6 µg/ml, in total volume of 150 µl. pAG/MNase was a gift from Steven Henikoff (Addgene plasmid #123461; http://n2t.net/addgene:123461; RRID: Addgene_123461), expressed and purified as described in (REF Meers 2019a). Samples were washed three times, followed by digestion for 30 min in wet ice in wash buffer supplemented with 2 mM CaCl2. 2X stop buffer (NaCl [340 mM], EDTA [20 mM], EGTA [4 mM], digitonin [0.05%], RNase A [100 µg/ml], glycogen [50 µl/ml]) was added to stop the reaction, and samples were incubated for 30 min at 37 °C. Beads were collected on the magnet and liquid transferred to a new tube. 2.5 µl proteinase K (Cat. #P8107S, New England BioLabs) and 2 µl 10% SDS were added, and samples incubated for 1 hr at 50 °C. Cells were washed three times in Nuclear Extraction (NE) buffer (HEPES-KOH pH-8.2 [20 mM], KCl [10 mM], Spermidine [0.5 mM], IGEPAL [0.05%], Glycerol [20%], Roche Complete Protease Inhibitor EDTA-Free), resuspended in 40 µl NE per sample and bound to 20 µl Magnetic ConA Agarose beads equilibrated in binding buffer. After incubation nuclei and beads are resuspended for 5 min in EDTA wash buffer (wash buffer with EDTA [0.2 mM]). Samples were divided in 200 µl PCR tubes and antibody incubation was performed in 200 µl wash buffer with 2 µl of antibody (for antibody and batch information, see Table 1) ON at 4 °C on a rotator. After ON incubation samples were washed 5 times in wash buffer and resuspended in 200 µl of pAG-MN buffer (wash buffer with pAG-MN 0.6 µg/ml) for 30 min at 4 °C on a rotator. Samples were washed five times, followed by digestion for 30 min in wet ice in wash buffer with 2 mM CaCl2. After 30 min the digestion buffer was removed and the reaction was stopped with 50 µl of 1X Urea STOP buffer (NaCl [100 mM], EDTA [2 mM], EGTA [2 mM], IGEPAL [0.5%], Urea [8.8 M]) and the samples were incubated 1 hr at 4°C. Beads were collected on the magnet and liquid transferred to a new PCR tube in which it was cleaned up twice using Mag-Bind TotalPure NGS beads (Cat. #M1327, Omega Bio-Tek) at 2X, and then resuspended in 20 µl Tris-HCl pH 7.5. Cells were washed three times in Nuclear Extraction (NE) buffer (HEPES-KOH pH-8.2 [20 mM], KCl [10 mM], Spermidine [0.5 mM], IGEPAL [0.05%], Glycerol [20%], Roche Complete Protease Inhibitor EDTA-Free), resuspended in 40 µl NE per sample and bound to 20 µl Magnetic ConA Agarose beads equilibrated in binding buffer. After incubation nuclei and beads are resuspended for 5 min in EDTA wash buffer (wash buffer with EDTA [0.2 mM]). Samples were divided in 200 µl PCR tubes and antibody incubation was performed in 200 µl wash buffer with 2 µl of antibody (for antibody and batch information, see Table 1) ON at 4 °C on a rotator. After ON incubation samples were washed 5 times in wash buffer and resuspended in 200 µl of pAG-MN buffer (wash buffer with pAG-MN 0.6 µg/ml) for 30 min at 4 °C on a rotator. Samples were washed five times, followed by digestion for 30 min in wet ice in wash buffer with 2 mM CaCl2. After 30 min the digestion buffer was removed and the reaction was stopped with 50 µl of 1X Urea STOP buffer (NaCl [100 mM], EDTA [2 mM], EGTA [2 mM], IGEPAL [0.5%], Urea [8.8 M]) and the samples were incubated 1 hr at 4°C. Beads were collected on the magnet and liquid transferred to a new PCR tube in which it was cleaned up twice using Mag-Bind TotalPure NGS beads (Cat. #M1327, Omega Bio-Tek) at 2X, and then resuspended in 20 µl Tris-HCl pH 7.5. Library preparation was performed using the KAPA Hyper Prep Kit for Illumina platforms (Cat. #KK8504, KAPA Biosystems) according to the manufacturer’s guidelines with the following modifications. End repair and A-tailing was performed with 0.4X volume reactions with 20 µl of purified DNA. The thermocycler conditions were set to 12 °C for 15 min, 37 °C for 15 min and 58 °C for 25 min to prevent thermal degradation of the shortest fragments. Adapter ligation was performed in 0.4X volume reactions. KAPA Dual Indexed adapters were used at 0.15 µM. A post-ligation clean-up was performed with Mag-Bind TotalPure NGS beads at 1.2X the sample volume. Resuspension was done in 10 mM Tris-HCl pH 8.0. Library amplification was performed in 0.5X volume reactions. The cycling conditions were set as follows: 45 sec initial denaturation at 98 °C, 15 sec denaturation at 98 °C, 10 sec annealing/elongation at 60 °C, 1 min final extension at 72 °C, hold at 4 °C, with 13 cycles. After amplification, a post-amplification cleanup was performed using NGS beads at 1.2X sample volume. Libraries were then run on an E-Gel EX 2% agarose gel (Cat. # G402022, Invitrogen) for 10 min using the E-Gel Power Snap Electrophoresis System (Invitrogen). Bands of interest between 150 and 500 bp were excised and purified using the GeneJET Gel Extraction Kit (Cat. #K0691, Thermo Scientific) according to manufacturer’s instructions.

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hindlimb

text: Mus musculus

text: JAX SWISS 034608


text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: embryonic day 11.5

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: branchial arches

text: Mus musculus

text: JAX SWISS 034608


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: heart

characteristic: organism part

text: Mus musculus

text: JAX SWISS 034608


characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: hindlimb

text: Mus musculus

text: JAX SWISS 034608

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

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text: house mouse

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: forelimb

text: Mus musculus

text: JAX SWISS 034608

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

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text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 11.5

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: branchial arches

text: Mus musculus

text: JAX SWISS 034608


characteristic: GISAID Accession ID

text: public

text: SIB

text: EHNV, CH-1400 Yverdon, Switzerland

characteristic: collecting institution

characteristic: collection date

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

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text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN13370/2022

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: INSDC center name

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text: public

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text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

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text: Human

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN12177/2022

characteristic: organism

text: active surveillance not initiated by an outbreak

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characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN12783/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

text: VD

text: Human

text: restricted access

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characteristic: host scientific name

text: restricted access

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN11471/2022

characteristic: isolate

characteristic: sample capture status


characteristic: GISAID Accession ID

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

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text: EHNV, CH-1400 Yverdon, Switzerland

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text: Switzerland

text: VD

text: Human

text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN13362/2022

characteristic: organism

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

text: public

text: SIB

text: Valais Hospital, Central Institute; Sion, Switzerland

characteristic: collection date

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text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

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text: restricted access

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text: Homo sapiens

text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN12787/2022


characteristic: GISAID Accession ID

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

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text: Human

text: restricted access

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characteristic: host scientific name

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text: hCoV-19/Switzerland/VD-CHUV-GEN13313/2022

characteristic: isolate

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

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text: SIB

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text: CHUV, CH-1011 Lausanne, Switzerland

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text: Switzerland

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text: hCoV-19/Switzerland/VD-CHUV-GEN13379/2022

characteristic: organism

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characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

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text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

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text: Homo sapiens

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text: hCoV-19/Switzerland/VD-CHUV-GEN11582/2022


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

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text: CHUV, CH-1011 Lausanne, Switzerland

text: Switzerland

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text: Human

text: restricted access

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characteristic: host scientific name

text: restricted access

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text: restricted access

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text: hCoV-19/Switzerland/VD-CHUV-GEN12795/2022

characteristic: isolate

characteristic: sample capture status


characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collecting institution

text: Switzerland

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text: Homo sapiens

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text: hCoV-19/Switzerland/VD-CHUV-GEN11473/2022

characteristic: organism

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characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: SIB

text: EHNV, CH-1400 Yverdon, Switzerland

characteristic: collection date

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13373/2022


characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/VD-CHUV-GEN12786/2022

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: EHNV, CH-1400 Yverdon, Switzerland

characteristic: collecting institution

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13315/2022

characteristic: organism

text: active surveillance in response to outbreak

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characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13360/2022

text: active surveillance not initiated by an outbreak


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

text: SIB

text: EHNV, CH-1400 Yverdon, Switzerland

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/VD-CHUV-GEN13384/2022

characteristic: isolate

characteristic: sample capture status


characteristic: GISAID Accession ID

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

characteristic: broker name

text: EHC MORGES, CH-1110 Morges, Switzerland

characteristic: collecting institution

text: Switzerland

text: VD

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13365/2022

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collection date

characteristic: collector name

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN13350/2022