characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 160

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: AGGAGTCCCTCTCTAT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

text: AATGATACGGCGACCACCGAGATCTACAC, CAAGCAGAAGACGGCATACGAGAT

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 20

text: Human

text: Lung

text: Sputum

text: United Kingdom

unit: DD

characteristic: geographic location (longitude)

unit: year

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: CATGCCTACTCTCTAT

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

text: Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease

characteristic: project name

unit: g

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 159

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

text: CCTCTCTGCTCTCTAT

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. kansasii

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 17

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: TGCCTCTTCTCTCTAT

characteristic: multiplex identifiers

text: FALSE

text: M. abscessus

text: TRUE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 27

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Control

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: TCCTCTACCTCTCTAT

text: FALSE

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 148

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: TTCTGCCTTATCCTCT

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 97

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

characteristic: lung/pulmonary disorder

text: GCTCAGGATATCCTCT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 85

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: AGGAGTCCTATCCTCT

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 34

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Control

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: CATGCCTATATCCTCT

text: FALSE

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 61

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: COPD

text: AGCGTAGCTATCCTCT

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

characteristic: lung/pulmonary disorder

text: CAGCCTCGTATCCTCT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 33

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: TCCTCTACTATCCTCT

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 133

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: CTAGTACGAGAGTAGA

text: TRUE

text: M. abscessus

text: TRUE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 28

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: TTCTGCCTAGAGTAGA

characteristic: multiplex identifiers

text: TRUE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 167

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: GCTCAGGAAGAGTAGA

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 68

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: GTAGAGAGAGAGTAGA

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: MAC

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: AATGATACGGCGACCACCGAGATCTACAC, CAAGCAGAAGACGGCATACGAGAT

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 25

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: CCTCTCTGAGAGTAGA

text: FALSE

text: M. avium complex

text: TRUE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 83

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: COPD

characteristic: lung/pulmonary disorder

text: AGCGTAGCAGAGTAGA

characteristic: multiplex identifiers

text: FALSE

text: M. xenopi

text: TRUE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: Yes

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

text: Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: M. xenopi

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 48

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Control

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: TCCTCTACAGAGTAGA

text: FALSE

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 135

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: CTAGTACGGTAAGGAG

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: Yes

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 149

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Control

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: TTCTGCCTGTAAGGAG

text: FALSE

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: Yes

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 40

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: GCTCAGGAGTAAGGAG

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 140

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: AGGAGTCCGTAAGGAG

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Extraction control

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: CATGCCTAGTAAGGAG

characteristic: multiplex identifiers

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 10

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: CCTCTCTGGTAAGGAG

text: FALSE

text: M. avium complex

text: TRUE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 91

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: AGCGTAGCGTAAGGAG

characteristic: multiplex identifiers

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: M. kansasii

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 142

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: TGCCTCTTGTAAGGAG

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 114

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: TCGCCTTAACTGCATA

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 136

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

characteristic: lung/pulmonary disorder

text: CTAGTACGACTGCATA

text: TRUE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 87

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: TTCTGCCTACTGCATA

characteristic: multiplex identifiers

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: M. kansasii

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Extraction control

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: CATGCCTAACTGCATA

text: Cowman et al. 2017

text: Cowman et al. 2017

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 36

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: CCTCTCTGACTGCATA

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: AATGATACGGCGACCACCGAGATCTACAC, CAAGCAGAAGACGGCATACGAGAT

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 92

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: AGCGTAGCACTGCATA

text: FALSE

text: M. abscessus

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: Yes

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. abscessus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 118

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: TCGCCTTAAAGGAGTA

characteristic: multiplex identifiers

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 86

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: GCTCAGGAAAGGAGTA

text: FALSE

text: M. malmoense

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease

text: human lung metagenome

text: Illumina Miseq

text: M. xenopi

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 89

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: AGGAGTCCAAGGAGTA

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: MAC

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 158

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: CATGCCTAAAGGAGTA

text: FALSE

text: M. avium complex

text: TRUE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 2

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: GTAGAGAGAAGGAGTA

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: MAC

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 41

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

text: CCTCTCTGAAGGAGTA

text: FALSE

text: M. kansasii

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. kansasii

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 113

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: AGCGTAGCAAGGAGTA

characteristic: multiplex identifiers

text: FALSE

text: M. abscessus

text: TRUE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No sample

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 7

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: TGCCTCTTAAGGAGTA

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No sample

characteristic: title


Neg

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Neg

text: human lung metagenome

text: Negative control

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: TCCTCTACAAGGAGTA

characteristic: multiplex identifiers

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

characteristic: target gene

text: Neg


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 120

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

characteristic: fvc

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: TCGCCTTACTAAGCCT

text: FALSE

text: M. abscessus

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: M. abscessus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 137

text: Human

text: Lung

text: Sputum

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: CTAGTACGCTAAGCCT

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 76

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: TTCTGCCTCTAAGCCT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: TRUE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 4

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: GCTCAGGACTAAGCCT

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: TRUE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: MAC

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 5

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: COPD

characteristic: lung/pulmonary disorder

text: AGGAGTCCCTAAGCCT

text: FALSE

text: M. fortuitum

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: No growth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: AATGATACGGCGACCACCGAGATCTACAC, CAAGCAGAAGACGGCATACGAGAT

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 143

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: COPD

text: CATGCCTACTAAGCCT

characteristic: multiplex identifiers

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 82

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Idiopathic bronchiectasis

characteristic: lung/pulmonary disorder

text: CCTCTCTGCTAAGCCT

text: FALSE

text: M. avium complex

text: FALSE

text: Cowman et al. 2017

text: Cowman et al. 2017

text: FALSE

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: MAC

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 144

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Case

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Secondary bronchiectasis

text: AGCGTAGCCTAAGCCT

characteristic: multiplex identifiers

text: FALSE

text: M. abscessus

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: FALSE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: M. abscessus

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Spontaneously expectorated sputum from subject 90

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Case

characteristic: host disease status

characteristic: host subject id

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: Secondary bronchiectasis

characteristic: lung/pulmonary disorder

text: CAGCCTCGCTAAGCCT

text: M. simiae

text: Cowman et al. 2017

text: Cowman et al. 2017

text: No

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: Profiling mycobacterial communities in pulmonary nontuberculous mycobacterial disease

text: human lung metagenome

text: Illumina Miseq

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NATIONAL HEART AND LUNG INSTITUTE, IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human lung metagenome

text: Spontaneously expectorated sputum from subject 21

text: Human

text: Lung

text: Sputum

characteristic: fvc

text: United Kingdom

characteristic: geographic location (longitude)

characteristic: host age

text: Control

text: human-associated

characteristic: human associated environmental package

text: metagenome

characteristic: investigation type

text: Cowman et al. 2017

characteristic: library construction method

text: Idiopathic bronchiectasis

text: TGCCTCTTCTAAGCCT

characteristic: multiplex identifiers

text: FALSE

text: FALSE

text: Cowman et al. 2017

characteristic: nucleic acid amplification

text: Cowman et al. 2017

characteristic: nucleic acid extraction

text: TRUE

text: No

text: human lung metagenome

text: TB11, TB12

characteristic: pcr primers

characteristic: project name

characteristic: sample volume or weight for DNA extraction

text: human lung metagenome

text: Illumina Miseq

characteristic: sequencing method

text: No growth

characteristic: target gene


Pos

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Pos

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: human lung metagenome

characteristic: common name

text: Positive control (mock community)

characteristic: description

text: Human

characteristic: environment (biome)

text: Lung

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: human-associated

text: metagenome

text: Cowman et al. 2017

text: TCCTCTACCTAAGCCT

text: Cowman et al. 2017

text: Cowman et al. 2017

text: human lung metagenome

characteristic: organism

text: TB11, TB12

text: human lung metagenome

text: Illumina Miseq

text: Pos

characteristic: title


E-MTAB-5970:casA-F3 -dCRI+sp8-1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Wadsworth Center, NYSDOH

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5970:casA-F3 -dCRI+sp8-1

tag: Namespace:The Wadsworth Center, NYSDOH

text: ArrayExpress

characteristic: broker name

text: Protocols: 2mL cultures were set up in LB, and grown for overnight at 37 degrees C/250rpm. Overnight cultures were subcultured 1:100 (+amp and 0.2% arabinose in the strains containing sp8 plasmid) and grown to an OD600 of 0.5-0.6 at 37 degrees. Cultures were crosslinked by adding formaldehyde to a final concentration of 1%, incubated for 20 minutes at room temperature, and quenched by adding glycine to a final concentration of 0.5 M. Cells were washed once in original culture volume of 1X TBS then washed again in 1 mL of 1X TBS. The supernatant was removed and the pellet was stored at -20 degrees C. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 2 uL anti-FLAG antibody (M2) were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10ul 10x quick blunting buffer, 10ul dNTP mix (kit supplied), 80ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3Õ->5Õexo-), from NEB: The samples were resuspended in the following mixture: 10ul 10X NEBuffer 2, 2ul 100mM dATP (NEB), 88ul dH2O, 2ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100ul 1x ligase buffer (50ul 2x buffer + 50ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR (7500 fast, ABI) with Illumina primers 1.1 and 2.1 (1uM ea). The manual ct was set to 0.1 and Ò3Ó was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number: 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. The following 50ul PCR reaction was used: 5ul 10x taq buffer, 8ul ChIP DNA with ligated adapters, 1.0 ul Illumina primer 1.1 (100uM), 1.0 ul Illumina primer 2.1 (100uM), 0.4 ul dNTP mix (25mM each), 1.5 ul taq, 33.6 ul dH2O. The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200bp to 500bp was cut out and gel purified. The bar-coded libraries were quantified using NEBNext kit and pooled at equimolar concentrations. Extraction and Library construction occur in the same protocol: Pelleted cells were resuspended in FA lysis buffer containing 2 mg/mL of lysozyme. Samples were incubated for 30 minutes at 37 degrees C, chilled on ice for at least 5 minutes, then sonicated for 30 minutes, with 30 s pulses followed by 30 s off. Samples were spun at maximum speed in a microcentrifuge, the supernatants were removed and diluted to 1 mL lysate per 20 mL original culture volume. Samples were immunoprecipitated according to the following procedure: for every 800 uL of chromatin, 25 uL of protein A beads (50% TBS slurry), and 2 uL anti-FLAG antibody (M2) were added. Samples were incubated on rotisserie rotater for 90 minutes at room temperature. Samples were then transferred to Spin-X columns (Corning) and washed twice with FA lysis buffer (150mM NaCl), 3 minutes each wash, rotating at room temperature. The samples were spun at 4000 rpm after each wash. The samples were then washed twice in the same way with 10 mM Tris-HCl, pH 7.5. The immunoprecipitated DNA, still attached to protein A beads, were then treated with Quick Blunting Kit (NEB): The samples were resuspended in the following mixture: 10ul 10x quick blunting buffer, 10ul dNTP mix (kit supplied), 80ul dH2O, 2ul blunt enzyme mix. The samples were incubated at room temperature, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 8.0. The samples were then A tailed, using Klenow (3Õ->5Õexo-), from NEB: The samples were resuspended in the following mixture: 10ul 10X NEBuffer 2, 2ul 100mM dATP (NEB), 88ul dH2O, 2ul Klenow. The samples were incubated at 37 degrees, while rotating, for 30 minutes. The samples were then washed twice with FA lysis buffer (150mM NaCl), as described above, and then washed twice with 10 mM Tris-HCl, pH 7.5. Illumina adapters were then ligated to the samples using the NEB Quick Ligation kit. The samples were resuspended in the following mixture: 100ul 1x ligase buffer (50ul 2x buffer + 50ul dH2O), 1 ul bracoded adapter, 4ul quick ligase. The samples were then incubated at room temperature, while rotating for 15 minutes. After incubation, the samples were washed, as decribed above, in the following buffers: FA lysis buffer; FA lysis buffer+500 mM NaCl; ChIP wash buffer; TE (10 mM Tris pH 8.0, 1 mM EDTA). Spin-X columns were transferred to a new microcentrifuge tube and 100 uL of ChIP elution buffer was added. Samples were incubated for 10 minutes at 65 degrees C then spun for 1 min at 1500 x g. Eluted DNA was then transferred to a new microcentrifuge tube and incubated for 10 minutes in a boiling water bath to de-crosslink samples. The samples were phenol extracted and ethanol precipitated. The samples were resuspended in 11ul. To determine cycle numbers for library amplification of each sample, 1ul ChIP DNA was used as a template (diluted 1/8 to fill 3 wells) for Real Time PCR (7500 fast, ABI) with Illumina primers 1.1 and 2.1 (1uM ea). The manual ct was set to 0.1 and Ò3Ó was added to the cycle number to determine the amount of cycles for library amplification. The ChIP DNA was used as a template, using the determined cycle number: 95 degrees for 30 seconds, 60 degrees for 30 seconds, 72 degrees for 30 seconds. The following 50ul PCR reaction was used: 5ul 10x taq buffer, 8ul ChIP DNA with ligated adapters, 1.0 ul Illumina primer 1.1 (100uM), 1.0 ul Illumina primer 2.1 (100uM), 0.4 ul dNTP mix (25mM each), 1.5 ul taq, 33.6 ul dH2O. The libraries were checked on an 8% non-denaturing acrylamide gel. The smear from 200bp to 500bp was cut out and gel purified. The bar-coded libraries were quantified using NEBNext kit and pooled at equimolar concentrations.

text: cas3 PcseI CRI + pLC008

characteristic: genotype

text: Escherichia coli str. K-12 substr. MG1655

text: casA-F3 -dCRI+sp8-1

type: has member


E-MTAB-5970:casA-F3 -dCRI+sp8-2

characteristic: External Id

text: The Wadsworth Center, NYSDOH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5970:casA-F3 -dCRI+sp8-2

characteristic: Submitter Id

text: ArrayExpress

text: cas3 PcseI CRI + pLC008

text: casA-F3 -dCRI+sp8-2


E-MTAB-5970:casA-F3 -dCRI-1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -dCRI-1

text: ArrayExpress

characteristic: description

text: cas3 PcseI CRI

text: casA-F3 -dCRI-1


E-MTAB-5970:casA-F3 -dCRI-2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -dCRI-2

text: ArrayExpress

text: cas3 PcseI CRI

text: casA-F3 -dCRI-2


E-MTAB-5970:casA-F3 -dCRII-1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -dCRII-1

text: ArrayExpress

text: cas3 PcseI CRII

text: casA-F3 -dCRII-1


E-MTAB-5970:casA-F3 -dCRII-2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -dCRII-2

text: ArrayExpress

text: cas3 PcseI CRII

text: casA-F3 -dCRII-2


E-MTAB-5970:casA-F3 -wt-1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -wt-1

text: ArrayExpress

text: cas3 PcseI

text: casA-F3 -wt-1


E-MTAB-5970:casA-F3 -wt-2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5970:casA-F3 -wt-2

text: ArrayExpress

text: cas3 PcseI

text: casA-F3 -wt-2


text: The Wadsworth Center, NYSDOH

text: public

text: ArrayExpress

text: cas3 PcseI + pCB381


text: The Wadsworth Center, NYSDOH

text: public

text: ArrayExpress

text: cas3 PcseI + pCB380


E-MTAB-5969:Plasmid loss cas3-1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss cas3-1

text: ArrayExpress

text: Protocols: • Start a 2 mL overnight for each Plasmid loss strain ( 13 different protospacer plasmids) in LB + Kan and amp at 37C, 225rpm. • Subculture all strains together into 10 mL of LB (12.5 L for 8 protospacers and 7.7 L for 13 protospacers) • Make electrocomp cells • Electroporate in pBAD33 and pBAD33-Cas3 WT into strains • Plate onto M9 + 0.2% glycerol + 0.2% arabinose + chloramphenicol carbenicillin • Next day: Scrape plates into 1.5 mL of LB, spin down, dump supernatant, and can freeze at -20 C here. pelleted cells were used as the source of DNA for PCR amplification o PCR protospacer with ultramers using a tiny bit of cells 40 L Taq Rxn, 68 anneal, 30 sec extension• Fwd: 1:10 dilution of 8567• Rev: 1:100 dilution of 8556-8566 and 8537

text: cas3::PcseI cas1 yggX::kan + pBAD33-wt cas3

characteristic: replicate

text: Plasmid loss cas3-1


E-MTAB-5969:Plasmid loss cas3-2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss cas3-2

text: ArrayExpress

text: Plasmid loss cas3-2


E-MTAB-5969:Plasmid loss cas3-3

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss cas3-3

text: ArrayExpress

text: Plasmid loss cas3-3


E-MTAB-5969:Plasmid loss empty-1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss empty-1

text: ArrayExpress

text: cas3::PcseI cas1 yggX::kan + empty pBAD33

text: Plasmid loss empty-1


E-MTAB-5969:Plasmid loss empty-2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss empty-2

text: ArrayExpress

text: Plasmid loss empty-2


E-MTAB-5969:Plasmid loss empty-3

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5969:Plasmid loss empty-3

text: ArrayExpress

text: Plasmid loss empty-3


text: public

tag: Namespace:Cancer Research UK - Cambridge Institute (CRUK-CI) and Department of Chemistry, University of Cambridge, UK

text: ArrayExpress

text: Protocols: TDG KO mice generation protocol: The Tdg-targeting construct (Supplementary Fig. 1) was generated by replacement of a NarI-PacI fragment enclosing exons 6 and 7 by a neomycin resistance cassette in a cloned fragment spanning exons 5-10 of the Tdg locus. This construct was used to target the Tdg allele in 129 mouse ESCs, which were then used to generate chimaeras and, ultimately, Tdg+/− heterozygotes by backcrossing to C57BL/6. Text taken from: doi:10.1038/nature09672 Breeding and tissue collection: Mice were maintained as heterozygotes and intercrossed to generate homozygous knockout embryos for analysis. Tissues were collected from timed matings with the day of the copulation plug as E0.5. Embryos were dissected into hindbrain, heart, liver and carcass.Text taken from: https://doi.org/10.1186/s13059-016-1001-5. NaBH4 was used to reduce 5-fC to 5-hmC as a control in the nucleosome reconstitution experiment (SLX-11454* samples) to demonstrate that MNase signal is derived from 5-fC. More details can be found in our previous work<http://www.nature.com/nchem/journal/v6/n5/full/nchem.1893.html>. NaBH3CN is a reducing agent which irreversibly traps out the Schiff base interactions (covalent bonds) between 5-fC and histone proteins. It was used in the polymerase stop assays (Polstop* samples). The concentration of NaBH3CN used was 100mM, the concentration where we had observed DNA-histone subunit cross-linking by gel electrophoresis. Genomic DNA and RNA was extracted from mouse embryonic tissues using the DNeasy Blood & Tissue kit (Qiagen). DNA library preparation for sequencing was done using the NEBNext DNA library preparation kit (New England Biolabs Inc.)

text: synthetic construct

text: synthetic construct

text: synthetic construct


text: Cancer Research UK - Cambridge Institute (CRUK-CI) and Department of Chemistry, University of Cambridge, UK

text: public

text: ArrayExpress

text: synthetic construct

text: synthetic construct

text: synthetic construct


text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain


E-MTAB-5971:MG1655 cas3 PcseI CRISPRI 1

characteristic: ENA-CHECKLIST

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5971:MG1655 cas3 PcseI CRISPRI 1

text: ArrayExpress

text: Protocols: 2mL overnights were grown in LB 37C at 225rpm and then subcultured 1:100. At an OD 0.5-0.7, RNA was harvested using the hot phenol method. Hot phenol RNA prep: transfer 1mL of subculture to microcentrifuge tube. Spin 1mL at max speed for 1 min and remove supernatant. Resuspend in 0.4mL ethanol+5% acid phenol/chloroform, spin 1 min at max speed and remove supernatant. Resuspend in 1mL 1x TBS, spin 1 min at max speed and remove supernatant. Resuspend in 0.5mL RNA Lysis Buffer (2% SDS, 4mM EDTA) and boil samples for 3 min. Add 0.5mL acid phenol/chloroform to each tube and incubate for 6 min at 65 °C. Incubate 5 min on ice then spin tubes at max speed for 6 min. Transfer upper phase to phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new phase lock tube, add equal volume (0.4mL) chloroform:isoamyl alcohol 24:1 and spin 6 min at max speed. Transfer upper phase to new tube containing 40uL 3M Na Acetate+2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. DNase treat RNA - set up 50uL reaction including 8-10ug RNA, 5uL of 10X buffer and 1uL DNase enzyme (Ambion). Incubate 30 min at 37 °C. Stop reaction by adding 352uL DEPC H2O + 134uL acid phenol:chloroform + 268uL chloroform:isoamyl alcohol 24:1. Transfer all to phase lock tube and spin at max speed for 6 min. Transfer upper phase to new microcentrifuge tube containing 40uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 1mL ice cold EtOH and precipitate at -20 °C overnight or 15min at -80 °C. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 15uL nuclease free water. Remove ribosomal RNA using the RiboZero kit from EpiCentre - wash magnetic beads 2x in RNase free water, then resuspend in Resuspension Solution. Add 32.5uL beads to each tube then add 0.5uL RNase inhibitor. Mix together in final volume of 20uL: 2.5ug DNase treated RNA + 2uL Ribozero reaction buffer + 4uL Ribozero rRNA removal solution. Incubate at 68 °C for 10 min followed by RT for 5 min. Add RNA to beads, mix by pipetting and vortexing for 10 s. Incubate at RT for 5 min. Vortex for 5 s then incubate at 50 °C for 5 min. Place tubes on magnetic stand for 1 min and transfer RNA to new tube. Bring volume to 180uL with DEPC H2O, then add 18uL 3M Na Acetate + 2uL glycogen (20mg/mL stock). Add 0.6mL ice cold EtOH and precipitate at -20 °C overnight. Spin samples for 30 min at 4 °C at max speed. Pipet off supernatant. Wash with 0.7mL of 70% EtOH (in DEPC H2O), spin 5 min at max speed at 4 °C and remove supernatant. Wash again with 0.7mL of 70% EtOH (in DEPC H2O), spin for 5 min at max speed at 4 °C and pipet off supernatant. Dry pellet at room temperature and resuspend in 8uL nuclease free water. Prepare libraries using EpiCentre ScriptSeq v2 kit following kit protocol. Fragment RNA and anneal cDNA synthesis primer in 12uL reaction containing nuclease free water + 40ng rRNA depleted RNA + 1uL RNA Fragmentation solution + 2uL cDNA Synthesis primer. Incubate at 85 °C for 5 min then place tubes on ice. Synthesize DNA by adding 3uL cDNA Synthesis Premix + 0.5uL 100mM DTT + 0.5uL StarScript Reverse Transcriptase. Incubate at 25 °C for 5 min then 42 °C for 20 min. Cool tubes to 37 °C. Add 1uL Finishing solution and incubate at 37 °C for 10 min then 95 °C for 3 min. Cool tubes to 25 °C then add 7.5uL Terminal Tagging Premix + 0.5uL DNA Polymerase to terminally tag the cDNA. Incubate at 25 °C for 15 min, 95 °C for 3 min, then cool to 4 °C. Purify the cDNA using the Qiagen MinElute PCR Purification Kit - Add 5V Buffer PB to sample and transfer all to MinElute column. Spin 1 min at max speed. Discard flow through. Add 0.75mL Buffer PE to column and spin 1 min at max speed. Discard flow through. Spin column for 1 min at max speed then transfer column to new tube. Add 23.4uL Buffer EB to column, incubate 1 min at room temp, then spin 1 min at max speed. Amplify library by setting up 50uL PCR using 22.5uL purified DNA. Add 25uL FailSafe PCR Premix E + 1uL Forward PCR primer + 1uL ScriptSeq Index PCR Primer + 0.5uL FailSafe PCR Enzyme (1.25U). Heat at 95 °C for 1 min, then 12 cycles of 95 °C for 30 sec, 55 °C for 30 sec and 68 °C for 3 min. Incubate at 68 °C for 7 minutes. Purify sample using AMPure XP Purification protocol. Add 50uL beads to each pcr sample. Mix by pipetting 10x. Transfer beads+sample to new tube and incubate at room temp for 15 min. Put tubes on magnetic stand for 5 min then remove supernatant. Wash beads 2x, each time with 0.2mL of 80% EtOH, let stand 1 min then remove supernatant. Air dry beads at room temp for 15 min. Add 12uL nuclease free water, remove tubes from magnetic stand and resuspend beads in water. Incubate at room temp for 2 min. Place tubes on magnetic stand for 5 min. Library is in supernatant. Transfer to new tube. Quantify using Qubit.

text: cas3 PcseI CRISPRI

characteristic: organism

text: MG1655 cas3 PcseI CRISPRI 1

characteristic: title


E-MTAB-5971:MG1655 cas3 PcseI CRISPRI 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: The Wadsworth Center, NYSDOH

text: public

characteristic: INSDC status

text: E-MTAB-5971:MG1655 cas3 PcseI CRISPRI 2

text: ArrayExpress

text: cas3 PcseI CRISPRI

text: MG1655 cas3 PcseI CRISPRI 2


E-MTAB-5971:MG1655 cas3 PcseI 1

text: The Wadsworth Center, NYSDOH

text: public

characteristic: SRA accession

text: E-MTAB-5971:MG1655 cas3 PcseI 1

text: ArrayExpress

characteristic: broker name

text: cas3 PcseI

characteristic: genotype

text: MG1655 cas3 PcseI 1


E-MTAB-5971:MG1655 cas3 PcseI 2

characteristic: External Id

text: The Wadsworth Center, NYSDOH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5971:MG1655 cas3 PcseI 2

text: ArrayExpress

text: cas3 PcseI

text: MG1655 cas3 PcseI 2


E-MTAB-5972:ChIP  library-seq IP 1

text: The Wadsworth Center, NYSDOH

characteristic: INSDC last update

text: public

text: E-MTAB-5972:ChIP library-seq IP 1

characteristic: Submitter Id

text: ArrayExpress

text: Protocols: 1. Grew ON’s of strains to electroporate plasmids intoa. Binding assays: C-NC yggX* casA-F3 with pBAD33 (camR) 2. Made electrocomp cells and transformed in plasmids (ampR)(100ng into 50 µl of cells).3. Start overnights of each strain + plasmid a. Subculture 1/100 in 5 ml LB for 8 protospacer plasmids or 3 ml of LB for 13 protospacer plasmids. Induce system with 0.2% arabinose. Grow to appropriate OD600 (typically 0.3-0.6).b. Mix 8 X 5 ml or 13 (pLC023-35) X3 ml of cultures together.c. Crosslink cells by adding formaldehyde to final concentration of 1% (~1 ml per 40 ml culture). Swirl flask to mix. Incubate for 20 min at room temperature.d. Quench formaldehyde by adding 10 ml of 2.5 M glycine per 40 ml culture [final] = 0.5 M (typically).e. Spin cells at full speed 10 minutes in bench-top centrifuge and discard supernatant. f. Resuspend in 40 ml TBS (original culture volume). Spin and discard supernatant again.g. Resuspend in 1 ml TBS. Spin in microcentrifuge, max speed, 1 min. Discard supernatant. Cells can be frozen at this point. 1. Grew ON’s of strains to electroporate plasmids intoa. Binding assays: C-NC yggX* casA-F3 with pBAD33 (camR) 2. Made electrocomp cells and transformed in plasmids (ampR)(100ng into 50 µl of cells).3. Start overnights of each strain + plasmid a. Subculture 1/100 in 5 ml LB for 8 protospacer plasmids or 3 ml of LB for 13 protospacer plasmids. Induce system with 0.2% arabinose. Grow to appropriate OD600 (typically 0.3-0.6).b. Mix 8 X 5 ml or 13 (pLC023-35) X3 ml of cultures together.c. Crosslink cells by adding formaldehyde to final concentration of 1% (~1 ml per 40 ml culture). Swirl flask to mix. Incubate for 20 min at room temperature.d. Quench formaldehyde by adding 10 ml of 2.5 M glycine per 40 ml culture [final] = 0.5 M (typically).e. Spin cells at full speed 10 minutes in bench-top centrifuge and discard supernatant. f. Resuspend in 40 ml TBS (original culture volume). Spin and discard supernatant again.g. Resuspend in 1 ml TBS. Spin in microcentrifuge, max speed, 1 min. Discard supernatant. Cells can be frozen at this point. Immunoprecipitation (with protein A beads) Do X2 for IP to get enough DNA1. Transfer 20 ul to fresh tube for Input DNA control2. Add 25 μl protein A beads (from 50% slurry in TBS)3. Add appropriate amount of antibody [2 anti-FLAG) 4. Incubate for 90 min at room temperature on rotisserie rotator.5. Spin IP mix for 1 minute in microcentrifuge at 4,000 rpm. Remove supernatant by aspiration. 6. Resuspend in 700 μl FA lysis buffer and transfer to Spin-X column filter. Incubate for 3 min at room temperature on rotisserie rotator. Spin (as before) and discard supernatant7. Wash with 750 μl of each of the below buffers by incubating for 3 min at room temperature on rotisserie rotator, spinning for 1 minute in microcentrifuge at 4,000 rpm and discarding supernatant:FA lysis bufferFA lysis buffer (again)FA lysis buffer + 500 mM NaCl, ChIP wash buffer, TE (10 mM Tris pH 8.0, 1 mM EDTA). 8. Place Spin-X filter in fresh dolphin-nosed tube. 9. Resuspend beads in 100 μl ChIP elution buffer and incubate for 10 min at 65 °C with occasional gentle mixing.10. Spin for 1 minute in microcentrifuge at 4,000 rpm. Discard filter.11. Transfer to normal 1.5 ml tube and incubate 10 min at 100 °C (Bring to rolling boil and then put at 380) to Decrosslink. Include 20 ul input sample (add 80 microliters ChIP elution buffer to total 100). 12. Clean up ChIP and Input DNA with Zymo PCR purification kit (use 2V of binding buffer), elute w/ 200 ul H2O for IC and 75 ul H2O per IP for a total of 150 ul H2O.6) Check concentrations with Qubita) 5 µL into 195 µL for ICb) 5 µL into 195 µL for IP Making Mi-seq libraryPCR• 5.48 ng of Chromatin from ChIP• 50 µL Failsafe Rxno 0.5 Failsafe, 0.5 fwd, 0.5 rev, Rest of 23.5 with dH2O, 25 Buffer “C” Ultramers: 1:10 8567 and 1:100 8556-8566 & 8537• 98° 2 min, (95° 30 sec, 72° 30 sec., 72° 30 sec. 25 cycles)0.8X Ampure bead clean-up, elute with 11µL dH2O, Qubit 1 microliter

characteristic: description

text: cas3::PcseI casA-FLAG3 yggX::kan + mix of 13 protospacer plasmids + pBAD33-wt cas3

text: ChIP library-seq IP 1


E-MTAB-5972:ChIP  library-seq IP 2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq IP 2

text: ArrayExpress

characteristic: replicate

text: ChIP library-seq IP 2


E-MTAB-5972:ChIP  library-seq IP 3

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq IP 3

text: ArrayExpress

text: ChIP library-seq IP 3


E-MTAB-5972:ChIP  library-seq IP 4

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq IP 4

text: ArrayExpress

text: ChIP library-seq IP 4


E-MTAB-5972:ChIP  library-seq IP 6

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq IP 6

text: ArrayExpress

text: ChIP library-seq IP 6


E-MTAB-5972:ChIP library-seq input 1

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq input 1

text: ArrayExpress

text: ChIP library-seq input 1


E-MTAB-5972:ChIP library-seq input 2

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq input 2

text: ArrayExpress

text: ChIP library-seq input 2


E-MTAB-5972:ChIP library-seq input 3

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq input 3

text: ArrayExpress

text: ChIP library-seq input 3


E-MTAB-5972:ChIP library-seq input 4

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq input 4

text: ArrayExpress

text: ChIP library-seq input 4


E-MTAB-5972:ChIP library-seq input 6

text: The Wadsworth Center, NYSDOH

text: public

text: E-MTAB-5972:ChIP library-seq input 6

text: ArrayExpress

text: ChIP library-seq input 6


text: LIMM

text: public

text: pre-antibiotic

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: clindamycin

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: germination

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: vancomycin

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: recurrence

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: fidaxomicin

text: metagenome

text: metagenome

text: gut model antibiotic study


text: LIMM

text: public

text: recovery

text: metagenome

text: metagenome

text: gut model antibiotic study