characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: NO

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

characteristic: body mass index

text: UBERON:sebum

text: UBERON:skin of arm

text: human skin metagenome

text: GAZ:Venezuela

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

text: human-associated habitat

text: sebum

text: human-associated

text: sebum

text: Yanomami

text: True

text: wife of 6

text: Venezuela:Alto Orinoco

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

text: Missing: Not collected

characteristic: life stage

text: Alto Orinoco

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Mahecoto

text: fever

text: Platanal


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: NO

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:feces

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:feces

characteristic: body site

text: human gut metagenome

characteristic: common name

text: GAZ:Venezuela

characteristic: country

characteristic: depth

characteristic: description

text: B fishing, hunting, cassava-yucuta, some maize and plantane, local í_fruits

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: village biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: Yanomami

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: wife of 6

characteristic: family relationship

text: Venezuela:Alto Orinoco

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not collected

text: Alto Orinoco

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: NO

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:mouth

characteristic: body mass index

text: UBERON:saliva

text: UBERON:mouth

text: human oral metagenome

text: GAZ:Venezuela

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: Yanomami

text: True

text: wife of 6

text: Venezuela:Alto Orinoco

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

text: Missing: Not collected

characteristic: life stage

text: Alto Orinoco

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: saliva

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: female

characteristic: sex

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: NO

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:vagina

characteristic: body habitat

text: UBERON:mucus

characteristic: body product

text: UBERON:vagina

characteristic: body site

text: human metagenome

characteristic: common name

text: GAZ:Venezuela

characteristic: country

characteristic: depth

characteristic: description

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: mucus

characteristic: env matter

text: human-vaginal

characteristic: env package

text: mucus

text: Yanomami

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: wife of 6

characteristic: family relationship

text: Venezuela:Alto Orinoco

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not collected

text: Alto Orinoco

text: Missing: Not provided

text: human vaginal metagenome

text: Boulder

text: True

text: True

text: completed

text: vaginal mucus

text: sequenced (16S)

text: human vaginal metagenome

text: female

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

characteristic: body mass index

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Child

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Child

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body mass index

text: UBERON:anal mucosa

text: UBERON:anus

text: Missing: Not provided

text: human gut metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

text: human-associated habitat

text: feces

text: human-gut

text: feces

text: MestizoHispano

text: True

text: Missing: Not provided

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Child

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human gut metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: stool

characteristic: sample type

text: sequenced (16S)

text: human gut metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: KE

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

characteristic: body habitat

text: UBERON:sebum

characteristic: body product

text: UBERON:skin of arm

characteristic: body site

text: human skin metagenome

characteristic: common name

text: GAZ:Venezuela

characteristic: country

characteristic: depth

characteristic: description

text: C fishing, hunting, cassava-yucuta, maize, plantane, local fruits, some market food

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: sebum

characteristic: env matter

text: human-associated

characteristic: env package

text: sebum

text: Yanomami

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

characteristic: family relationship

text: Venezuela:Alto Orinoco

text: g/L

text: human

text: Homo sapiens

text: Missing: Not collected

text: Alto Orinoco

text: Missing: Not provided

text: human skin metagenome

text: Boulder

text: True

text: True

text: completed

text: skin

text: sequenced (16S)

text: human skin metagenome

text: male

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: KE

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:feces

characteristic: body mass index

text: UBERON:feces

text: UBERON:feces

text: human gut metagenome

text: GAZ:Venezuela

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

text: human-associated habitat

text: feces

text: human-gut

text: feces

text: Yanomami

text: True

text: Missing: Not provided

text: Venezuela:Alto Orinoco

characteristic: geo loc name

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

text: Missing: Not collected

characteristic: life stage

text: Alto Orinoco

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human gut metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: stool

characteristic: sample type

text: sequenced (16S)

text: human gut metagenome

text: male

characteristic: sex

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

text: KE

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:nostril

characteristic: body habitat

text: UBERON:mucus

characteristic: body product

text: UBERON:nasal mucosa

characteristic: body site

text: human nasal/pharyngeal metagenome

characteristic: common name

text: GAZ:Venezuela

characteristic: country

characteristic: depth

characteristic: description

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: village biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: mucus

characteristic: env matter

text: human-associated

characteristic: env package

text: mucus

text: Yanomami

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

characteristic: family relationship

text: Venezuela:Alto Orinoco

text: g/L

text: human

text: Homo sapiens

text: Missing: Not collected

text: Alto Orinoco

text: Missing: Not provided

text: human nasal/pharyngeal metagenome

text: Boulder

text: True

text: True

text: completed

text: nasal mucus

text: sequenced (16S)

text: human nasal/pharyngeal metagenome

text: male

text: Mahecoto

text: fever

text: Platanal


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: altitude

characteristic: anonymized name

text: True

text: unclassified metagenome

text: GAZ:United States of America

text: True

text: EMP sample

text: Control

text: Negative

text: Sterile water blank

text: urban biome

text: research facility

text: sterile water

text: misc environment

text: sterile water

text: True

text: USA:CO:Boulder:not applicable

characteristic: geo loc name

characteristic: host subject id

characteristic: host taxid

characteristic: latitude

characteristic: longitude

text: metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: control blank

characteristic: sample type

text: sequenced (16S)

text: metagenome

characteristic: title

type: has member


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

text: public

text: True

text: unclassified metagenome

characteristic: common name

text: GAZ:United States of America

characteristic: country

characteristic: depth

characteristic: description

text: True

characteristic: elevation

text: EMP sample

text: Control

text: Negative

text: Sterile water blank

text: urban biome

characteristic: env biome

text: research facility

characteristic: env feature

text: sterile water

characteristic: env matter

text: misc environment

characteristic: env package

text: sterile water

text: True

characteristic: extracted DNA avail now

text: USA:CO:Boulder:not applicable

text: metagenome

text: Boulder

text: True

text: True

text: completed

text: control blank

text: sequenced (16S)

text: metagenome


text: UCSDMI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:breast

characteristic: body habitat

characteristic: body mass index

text: UBERON:mammary gland milk

characteristic: body product

text: UBERON:mammary gland

characteristic: body site

text: Missing: Not provided

text: human metagenome

text: GAZ:Puerto Rico

text: W western

characteristic: diet

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: breast milk

text: human-associated

text: breast milk

text: MestizoHispano

characteristic: ethnic group

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Adult

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: breast milk

characteristic: sample type

text: sequenced (16S)

text: human metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

characteristic: body mass index

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Adult

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:skin

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Adult

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

characteristic: body mass index

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Adult

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:vagina

text: UBERON:mucus

text: UBERON:skin of arm

text: Missing: Not provided

text: human metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: mucus

text: human-vaginal

text: mucus

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Adult

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human vaginal metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: vaginal mucus

characteristic: sample type

text: sequenced (16S)

text: human vaginal metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

characteristic: body mass index

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: C-section

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

text: Missing: Not collected

characteristic: body mass index

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: BB breast milk and BS baby solids

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: male

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

text: Missing: Not collected

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: BB breast milk/W western W westernestern diet

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Missing: Not provided

characteristic: shabono

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

text: Missing: Not collected

characteristic: body mass index

text: UBERON:saliva

text: UBERON:mouth

text: Missing: Not provided

text: human oral metagenome

text: GAZ:Puerto Rico

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: saliva

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:breast

characteristic: body habitat

characteristic: body mass index

text: UBERON:sebum

characteristic: body product

text: UBERON:areola

characteristic: body site

text: Missing: Not provided

text: human skin metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: sebum

characteristic: env matter

text: human-skin

characteristic: env package

text: sebum

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Adult

text: San Juan

text: Missing: Not provided

text: human skin metagenome

text: Boulder

text: True

text: True

text: completed

text: skin

text: sequenced (16S)

text: human skin metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

text: Missing: Not collected

text: UBERON:saliva

text: UBERON:mouth

text: Missing: Not provided

text: human oral metagenome

text: GAZ:Puerto Rico

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Child

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: saliva

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: male

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

characteristic: body habitat

text: Missing: Not collected

characteristic: body mass index

text: UBERON:sebum

characteristic: body product

text: UBERON:skin of arm

characteristic: body site

text: Missing: Not provided

text: human skin metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: sebum

characteristic: env matter

text: human-skin

characteristic: env package

text: sebum

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Child

text: San Juan

text: Missing: Not provided

text: human skin metagenome

text: Boulder

text: True

text: True

text: completed

text: skin

text: sequenced (16S)

text: human skin metagenome

text: male

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: C-section

characteristic: birth

text: UBERON:skin

text: Missing: Not collected

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: BB breast milk and BS

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: male

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: C-section

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: BB breast milk and BS

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: male

text: Missing: Not provided

characteristic: shabono

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:gastrointestinal system

text: UBERON:feces

text: UBERON:rectum

text: Missing: Not provided

text: human gut metagenome

text: GAZ:Puerto Rico

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

text: human-associated habitat

text: feces

text: human-gut

text: feces

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Child

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human gut metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: stool

characteristic: sample type

text: sequenced (16S)

text: human gut metagenome

text: male

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

characteristic: body mass index

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

text: Missing: Not collected

text: UBERON:saliva

text: UBERON:mouth

text: Missing: Not provided

text: human oral metagenome

text: GAZ:Puerto Rico

text: BB breast milk and W western W westernestern diet

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: saliva

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

characteristic: body mass index

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Adult

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:skin

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Adult

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

characteristic: body mass index

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Adult

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: Missing: Not collected

characteristic: birth

text: UBERON:vagina

text: UBERON:mucus

text: UBERON:skin of arm

text: Missing: Not provided

text: human metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: mucus

text: human-vaginal

text: mucus

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Adult

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human vaginal metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: vaginal mucus

characteristic: sample type

text: sequenced (16S)

text: human vaginal metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

characteristic: body habitat

text: Missing: Not collected

characteristic: body mass index

text: UBERON:saliva

characteristic: body product

text: UBERON:mouth

characteristic: body site

text: Missing: Not provided

text: human oral metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: BB breast milk

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: saliva

characteristic: env matter

text: human-oral

characteristic: env package

text: saliva

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human oral metagenome

text: Boulder

text: True

text: True

text: completed

text: saliva

text: sequenced (16S)

text: human oral metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

text: Missing: Not collected

text: UBERON:sebum

text: UBERON:skin of arm

text: Missing: Not provided

text: human skin metagenome

text: GAZ:Puerto Rico

text: BB breast milk

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: sebum

text: human-skin

text: sebum

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human skin metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human skin metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:gastrointestinal system

characteristic: body habitat

text: UBERON:feces

characteristic: body product

text: UBERON:rectum

characteristic: body site

text: Missing: Not provided

text: human gut metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: BB breast milk

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal distal gut

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: feces

characteristic: env matter

text: human-gut

characteristic: env package

text: feces

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human gut metagenome

text: Boulder

text: True

text: True

text: completed

text: stool

text: sequenced (16S)

text: human gut metagenome

text: female

text: Missing: Not provided

characteristic: shabono

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:oral cavity

characteristic: body mass index

text: UBERON:saliva

text: UBERON:mouth

text: Missing: Not provided

text: human oral metagenome

text: GAZ:Puerto Rico

text: W western

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: saliva

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: female

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: natural

characteristic: birth

text: UBERON:skin

characteristic: body habitat

characteristic: body mass index

text: UBERON:sebum

characteristic: body product

text: UBERON:skin of arm

characteristic: body site

text: Missing: Not provided

text: human skin metagenome

characteristic: common name

text: GAZ:Puerto Rico

characteristic: country

characteristic: depth

characteristic: description

text: W western

characteristic: diet

text: True

characteristic: elevation

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

characteristic: env biome

text: human-associated habitat

characteristic: env feature

text: sebum

characteristic: env matter

text: human-skin

characteristic: env package

text: sebum

text: MestizoHispano

characteristic: ethnic group

text: True

characteristic: extracted DNA avail now

text: Missing: Not provided

text: Puerto Rico:San Juan

text: Missing: Not provided

text: g/L

text: human

text: Homo sapiens

text: Missing: Not provided

text: Infant

text: San Juan

text: Missing: Not provided

text: human skin metagenome

text: Boulder

text: True

text: True

text: completed

text: skin

text: sequenced (16S)

text: human skin metagenome

text: female

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: years

characteristic: age unit

characteristic: altitude

characteristic: anonymized name

text: True

text: C-section

characteristic: birth

text: UBERON:oral cavity

text: Missing: Not collected

text: UBERON:saliva

text: UBERON:mouth

text: Missing: Not provided

text: human oral metagenome

text: GAZ:Puerto Rico

text: BB breast milk and BS baby solids

text: True

text: EMP sample

text: Host associated

text: Animal

text: Animal secretion

text: urban biome

text: human-associated habitat

text: saliva

text: human-oral

text: saliva

text: MestizoHispano

text: True

text: Missing: Not provided

characteristic: family relationship

text: Puerto Rico:San Juan

characteristic: geo loc name

text: Missing: Not provided

characteristic: hb

text: g/L

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: host subject id

characteristic: host taxid

text: Missing: Not provided

characteristic: latitude

text: Infant

characteristic: life stage

text: San Juan

characteristic: location

characteristic: longitude

text: Missing: Not provided

characteristic: malaria

text: human oral metagenome

characteristic: organism

text: Boulder

text: True

text: True

characteristic: public

text: completed

text: skin

characteristic: sample type

text: sequenced (16S)

text: human oral metagenome

text: male

characteristic: sex

text: Missing: Not provided

text: Missing: Not provided

text: San Juan


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UQ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Australia

characteristic: geographic location (country and/or sea)

text: Brisbane

characteristic: geographic location (region and locality)

characteristic: isolate

text: Sputum

characteristic: isolation source

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

characteristic: strain

characteristic: sub strain

text: Sub-lineage of P. aeruginosa strain AUST-02 associated with increased antibiotic resistance.

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UQ

text: public

text: Outgroup to M3L7 strains. Typed as M3L1.

characteristic: description

text: Australia

text: Brisbane

text: Sputum

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

text: Sub-lineage of P. aeruginosa strain AUST-02


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TGAC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: bread wheat

characteristic: common name

text: Cadenza

characteristic: cultivar

text: Triticum aestivum

characteristic: sample name

text: Triticum aestivum

text: individual from the Cadenza TILLING population


text: ETH Zurich Institute of Biochemistry

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:ETH Zurich Institute of Biochemistry

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: Protocols: ade2Δ strains were transformed with the pBK257 plasmid. These strains are phenotypically ade-, since the ADE2 gene borne on the plasmid is interrupted by the miniDs transposon. 1 liter of freshly prepared SC -Ura +2% Raffinose + 0.2% Dextrose is inoculated with ade2Δ cells freshly transformed with pBK257, directly scraped off the transformation plates, at a final OD600=0.15. The culture is grown to saturation for 18 to 24hr at 30°C. Cells are spun for 5min at 600x g, 20°C) and resuspended in their supernatant at a final OD600=37. 200 μl of this resuspension are plated on ~250-300 X 8.5cm plates containing 25 ml of SC +2%Galactose -Adenine using glass beads. Plates are incubated in closed but not sealed plastic bags for 3 weeks at 30°C. Clones in which transposon excision has led to the repair of the ADE2 gene on pBK257 start to appear after 10-12 days. The density of clones on the plate reaches 150-200 colonies/cm2, i.e.8000-11000 colonies/plates after 3 weeks. All colonies are then scraped off the plates using minimal volume of either water or SD +2% dextrose -Adenine, pooled, and used to inoculate 2L SD +2%Dextrose -Adenine culture at a density of 2.5 106 cells/ml, which is allowed to grow to saturation. This step is used to dilute any remaining ade- cells, which represent about 20% of the total number of cells, and ensures that each transposition event is well represented. For example, reseeding a 2.106 clones library in 2L at a density of 2.5 106 cells/ml will ensure that each clone is represented by ((2.500.000X1000X2)*0.8)/2.000.000= 2000 cells. The saturated culture is harvested by centrifugation (5 min, 2500x g, 4°C), washed with ddH2O, then cell pellets are frozen as ~500 mg aliquots. A 500 mg cell pellet is resuspended with 500 μl Cell Breaking Buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 100 mM Tris-HCl pH8.0, 1 mM EDTA) and distributed in 280μl aliquots. 200 μl Phenol:Chloroform:Isoamylalcool 25:25:1 and 300 μl glass 0.4-0.6mm unwashed glass beads are added to each aliquot. Samples are vortexed for 10 min at 4°C using a Disruptor Genie from Scientific Industrial (US Patent 5,707,861). 200 μl TE are added to each lysate, which are then centrifuged for 5 min at 16100x g, 4°C. The upper layer (~400 μl) is transferred to a fresh tube, 2.5vol 100% EtOH are added and the sample mixed by inverted. DNA is pelleted for 5 min at 16100x g, 20°C. The supernatant is removed and the pellets resuspended in 200 μl RNAse A 250 μg/ml for 15 min at 55°C, 1000 rpm on a Thermomixer comfort (Eppendorf). 2.5 vol 100% EtOH and 0.1vol NaOAc 3 M pH5.2 are added and the samples mixed by inversion. DNA is pelleted by centrifugation for 5 min at 16100x g, 20°C. The pellets are washed with 70% EtOH under the same conditions, the supernatant removed completely, and the pellets let dry for 10 min at 37°C. The pellets are resuspended in a total volume of 100 μl water for 10 min at 55°C, 700 rpm on a Thermomixer comfort (Eppendorf). DNA is run on a 0.6% 1X TBE agarose gel against a standard 1 kb GeneRuler, and quantified using FiJi. 500mg cell pellet should yield approximately 10 μg DNA. Sequencing involves the following steps: 1-Digestion of genomic DNA with two four-cutter restriction enzymes, 2-ligase-mediated circularization of the DNA, 3-PCR of the transposon-genome junctions using outward-facing primers. 4-Illumina-sequencing of the combined PCR products. 2x 2 μg of genomic DNA are digested in parallel in Non-Stick microfuge tubes (Ambion AM12450) with 50 units of DpnII (NEB #R0543L) and NlaIII (NEB #R0125L), in 50 μl for 16 hours at 37°C. The reactions are then heat inactivated at 65°C for 20 min and circularized in the same tube by ligation with 25 Weiss units T4 Ligase (Thermo Scientific #EL0011) for 6 hours at 22°C, in a volume of 400μl. DNA is precipitated overnight or longer at -20°C in 0.3 M NaOAc pH5.2, 1 ml 100% EtOH, using 5 μg linear acrylamide (Ambion AM9520) as a carrier, then centrifuged for 20 min at 16100x g, 4°C. Pellets are washed with 1 ml 70% EtOH, for 20 min at 16100 x g, 20°C. After complete removal of the supernatant, pellets are dried for 10 min at 37°C. Each circularized DNA preparation is then resuspended in water and divided into 10X 100 μl PCR reactions. Each 100 μl PCR reaction contains: 10 μl 10X Taq Buffer (500 mM Tris-HCl pH9.2, 22.5 mM MgCl2, 160 mM NH4SO4, 20% DMSO, 1% Triton X-100 - stored at -20°C), 20 μM dNTPs, 1 μM primer #1, 1 μM primer #2 , 2.4 μl homemade Taq polymerase. PCR are performed in an MJ Research Peltier Thermal Cycler PTC-200 using the following conditions: Block: calculated - 95°C 1 min, 35X [95°C 30 sec, 55°C 30 sec, 72°C 3 min], 72°C 10 min. The 2X10 PCR reactions are pooled into one NlaIII-digested pool and one DpnII-digested pool. 100μl of each pool are purified using a PCR clean-up/gel extraction kit (Macherey-Nagel) according to the manufacturer protocol, with the following modifications: binding of DNA: 30s at 3000x g; elution: 30 μl of (10 mM Tris-HCl pH8.5, 0.1% Tween) are applied to the column and let sit for 3 min, then sample is spun for 1 min 11000x g at 20°C. The eluate is reapplied to the column and a second elution is performed under the same conditions. Purified PCR products are quantified by absorbance at 260 nm. On a 1% agarose gel, the product runs as a smear from 250bp to 1.2 kb, with highest density centered around 500bp. The 867 bp size band present in the NlaIII treated sample and the 465 bp size band present in the DpnII treated sample correspond to untransposed pBK257.

characteristic: genotype

text: normal

characteristic: growth condition

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: ETH Zurich Institute of Biochemistry

text: public

text: ArrayExpress

text: baker's yeast

text: wild type genotype

text: normal

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

characteristic: title


characteristic: ENA-LAST-UPDATE

text: ETH Zurich Institute of Biochemistry

text: public

text: ArrayExpress

text: baker's yeast

text: Protocols: ade2Δ strains were transformed with the pBK257 plasmid. These strains are phenotypically ade-, since the ADE2 gene borne on the plasmid is interrupted by the miniDs transposon. 1 liter of freshly prepared SC -Ura +2% Raffinose + 0.2% Dextrose is inoculated with ade2Δ cells freshly transformed with pBK257, directly scraped off the transformation plates, at a final OD600=0.15. The culture is grown to saturation for 18 to 24hr at 30°C. Cells are spun for 5min at 600x g, 20°C) and resuspended in their supernatant at a final OD600=37. 200 μl of this resuspension are plated on ~250-300 X 8.5cm plates containing 25 ml of SC +2%Galactose -Adenine using glass beads. Plates are incubated in closed but not sealed plastic bags for 3 weeks at 30°C. Clones in which transposon excision has led to the repair of the ADE2 gene on pBK257 start to appear after 10-12 days. The density of clones on the plate reaches 150-200 colonies/cm2, i.e.8000-11000 colonies/plates after 3 weeks. All colonies are then scraped off the plates using minimal volume of either water or SD +2% dextrose -Adenine, pooled, and used to inoculate 2L SD +2%Dextrose -Adenine culture at a density of 2.5 106 cells/ml, which is allowed to grow to saturation. This step is used to dilute any remaining ade- cells, which represent about 20% of the total number of cells, and ensures that each transposition event is well represented. For example, reseeding a 2.106 clones library in 2L at a density of 2.5 106 cells/ml will ensure that each clone is represented by ((2.500.000X1000X2)*0.8)/2.000.000= 2000 cells. The saturated culture is harvested by centrifugation (5 min, 2500x g, 4°C), washed with ddH2O, then cell pellets are frozen as ~500 mg aliquots. Cells scraped off the plates were used to inoculate a 1 liter SC +2%Dextrose -Adenine culture at a density of 2.5x 106 cells/ml. After growing for 12-14 h to OD 0.5, the culture was diluted to OD 0.1 in 500 ml SD+2%Dextrose -Adenine, treated with 10 nM rapamycin (Sigma) and grown to saturation overnight. Next morning, the saturated culture was diluted again to OD 0.1 in 500 ml SD +2%Dextrose -Adenine +10 nM rapamycin. The treated culture was again grown to saturation overnight, harvested by centrifugation and processed for genomic DNA extraction. A 500 mg cell pellet is resuspended with 500 μl Cell Breaking Buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 100 mM Tris-HCl pH8.0, 1 mM EDTA) and distributed in 280μl aliquots. 200 μl Phenol:Chloroform:Isoamylalcool 25:25:1 and 300 μl glass 0.4-0.6mm unwashed glass beads are added to each aliquot. Samples are vortexed for 10 min at 4°C using a Disruptor Genie from Scientific Industrial (US Patent 5,707,861). 200 μl TE are added to each lysate, which are then centrifuged for 5 min at 16100x g, 4°C. The upper layer (~400 μl) is transferred to a fresh tube, 2.5vol 100% EtOH are added and the sample mixed by inverted. DNA is pelleted for 5 min at 16100x g, 20°C. The supernatant is removed and the pellets resuspended in 200 μl RNAse A 250 μg/ml for 15 min at 55°C, 1000 rpm on a Thermomixer comfort (Eppendorf). 2.5 vol 100% EtOH and 0.1vol NaOAc 3 M pH5.2 are added and the samples mixed by inversion. DNA is pelleted by centrifugation for 5 min at 16100x g, 20°C. The pellets are washed with 70% EtOH under the same conditions, the supernatant removed completely, and the pellets let dry for 10 min at 37°C. The pellets are resuspended in a total volume of 100 μl water for 10 min at 55°C, 700 rpm on a Thermomixer comfort (Eppendorf). DNA is run on a 0.6% 1X TBE agarose gel against a standard 1 kb GeneRuler, and quantified using FiJi. 500mg cell pellet should yield approximately 10 μg DNA. Sequencing involves the following steps: 1-Digestion of genomic DNA with two four-cutter restriction enzymes, 2-ligase-mediated circularization of the DNA, 3-PCR of the transposon-genome junctions using outward-facing primers. 4-Illumina-sequencing of the combined PCR products. 2x 2 μg of genomic DNA are digested in parallel in Non-Stick microfuge tubes (Ambion AM12450) with 50 units of DpnII (NEB #R0543L) and NlaIII (NEB #R0125L), in 50 μl for 16 hours at 37°C. The reactions are then heat inactivated at 65°C for 20 min and circularized in the same tube by ligation with 25 Weiss units T4 Ligase (Thermo Scientific #EL0011) for 6 hours at 22°C, in a volume of 400μl. DNA is precipitated overnight or longer at -20°C in 0.3 M NaOAc pH5.2, 1 ml 100% EtOH, using 5 μg linear acrylamide (Ambion AM9520) as a carrier, then centrifuged for 20 min at 16100x g, 4°C. Pellets are washed with 1 ml 70% EtOH, for 20 min at 16100 x g, 20°C. After complete removal of the supernatant, pellets are dried for 10 min at 37°C. Each circularized DNA preparation is then resuspended in water and divided into 10X 100 μl PCR reactions. Each 100 μl PCR reaction contains: 10 μl 10X Taq Buffer (500 mM Tris-HCl pH9.2, 22.5 mM MgCl2, 160 mM NH4SO4, 20% DMSO, 1% Triton X-100 - stored at -20°C), 20 μM dNTPs, 1 μM primer #1, 1 μM primer #2 , 2.4 μl homemade Taq polymerase. PCR are performed in an MJ Research Peltier Thermal Cycler PTC-200 using the following conditions: Block: calculated - 95°C 1 min, 35X [95°C 30 sec, 55°C 30 sec, 72°C 3 min], 72°C 10 min. The 2X10 PCR reactions are pooled into one NlaIII-digested pool and one DpnII-digested pool. 100μl of each pool are purified using a PCR clean-up/gel extraction kit (Macherey-Nagel) according to the manufacturer protocol, with the following modifications: binding of DNA: 30s at 3000x g; elution: 30 μl of (10 mM Tris-HCl pH8.5, 0.1% Tween) are applied to the column and let sit for 3 min, then sample is spun for 1 min 11000x g at 20°C. The eluate is reapplied to the column and a second elution is performed under the same conditions. Purified PCR products are quantified by absorbance at 260 nm. On a 1% agarose gel, the product runs as a smear from 250bp to 1.2 kb, with highest density centered around 500bp. The 867 bp size band present in the NlaIII treated sample and the 465 bp size band present in the DpnII treated sample correspond to untransposed pBK257.

characteristic: description

text: wild type genotype

text: rapamycin

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: WT+rapamycin


E-MTAB-4855:Sample 1

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-4855:Sample 1

tag: Namespace:University of Groningen, Genomics Research in Ecology & Evolution in Nature (GREEN) - Plant Physiology, Groningen Institute for Evolutionary Life Sciences (GELIFES)

text: ArrayExpress

text: Protocols: Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini-Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net).

text: optimal temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

characteristic: organism part

text: Solanum habrochaites

text: Sample 1


E-MTAB-4855:Sample 10

text: University of Groningen, Genomics Research in Ecology & Evolution in Nature (GREEN) - Plant Physiology, Groningen Institute for Evolutionary Life Sciences (GELIFES)

characteristic: INSDC last update

text: public

text: E-MTAB-4855:Sample 10

text: ArrayExpress

text: tomato

characteristic: common name

text: Moneymaker

characteristic: cultivar

text: cold temperature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: whole root

text: Solanum lycopersicum

text: Sample 10


E-MTAB-4855:Sample 11

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-4855:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: tomato

text: Moneymaker

text: cold temperature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: whole root

text: Solanum lycopersicum

text: Sample 11


E-MTAB-4855:Sample 12

text: public

text: E-MTAB-4855:Sample 12

text: ArrayExpress

characteristic: broker name

text: tomato

text: Moneymaker

text: cold temperature

characteristic: growth condition

text: Solanum lycopersicum

text: Solanum lycopersicum

text: whole root

text: Solanum lycopersicum

text: Sample 12


E-MTAB-4855:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-4855:Sample 2

text: ArrayExpress

text: optimal temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

text: Solanum habrochaites

text: Sample 2


E-MTAB-4855:Sample 3

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-4855:Sample 3

text: ArrayExpress

text: optimal temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

text: Solanum habrochaites

text: Sample 3

characteristic: title


E-MTAB-4855:Sample 4

text: public

text: E-MTAB-4855:Sample 4

text: ArrayExpress

text: tomato

text: Moneymaker

characteristic: description

text: optimal temperature

text: Solanum lycopersicum

characteristic: organism

text: Solanum lycopersicum

text: whole root

text: Solanum lycopersicum

text: Sample 4


E-MTAB-4855:Sample 5

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-4855:Sample 5

text: ArrayExpress

text: tomato

text: Moneymaker

text: optimal temperature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: whole root

text: Solanum lycopersicum

text: Sample 5


E-MTAB-4855:Sample 6

characteristic: INSDC first public

text: public

text: E-MTAB-4855:Sample 6

text: ArrayExpress

text: tomato

text: Moneymaker

text: optimal temperature

text: Solanum lycopersicum

text: Solanum lycopersicum

text: whole root

characteristic: organism part

text: Solanum lycopersicum

text: Sample 6


E-MTAB-4855:Sample 7

characteristic: INSDC last update

text: public

text: E-MTAB-4855:Sample 7

text: ArrayExpress

text: cold temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

text: Solanum habrochaites

text: Sample 7


E-MTAB-4855:Sample 8

text: public

text: E-MTAB-4855:Sample 8

text: ArrayExpress

characteristic: cultivar

text: cold temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

text: Solanum habrochaites

text: Sample 8


E-MTAB-4855:Sample 9

text: public

characteristic: INSDC status

text: E-MTAB-4855:Sample 9

text: ArrayExpress

text: cold temperature

text: Solanum habrochaites

text: Solanum habrochaites

text: whole root

text: Solanum habrochaites

text: Sample 9


text: public

characteristic: SRA accession

tag: Namespace:Program in Genetics and Genome Biology, the Hospital for Sick Children, Department of Molecular Genetics, University of Toronto

text: ArrayExpress

text: endothelial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Chromatin immunoprecipitation experiments were conducted as previously described in (Schmidt et al. 2009). Antibodies used for ChIP were mouse anti-H3K27ac (Millipore, 05-1334 monoclonal) and rabbit anti-Jun (Santa Cruz Biotechnology, sc1694 polyclonal). EC were grown in supplier-recommended Endothelial Cell Growth Media (Cell Applications, catalogue #211-500) and cultured at 37° C in a 5%-CO2 humidified incubator. ChIP DNA was prepared for Illumina sequencing by blunt-end repair, dA-tailing, and ligation of Illumina adaptors using a NEBNext DNA library preparation kit (New England Biolabs, catalogue #E6040L). Total ChIP DNA (approximately 200-500ng) and 220ng of DNA input (WCE) was end repaired for 30 minutes at room temperature, and then purified using column purification with either DNA Clean and Concentrator (Zymogen, catalogue #D4014) or PCR purification columns (Qiagen, catalogue #28106) as recommended by manufacturer’s protocol. Blunt-end repaired DNA was dA-tailed for 40 minutes at 37° C, then column purified. dA-tailed DNA was ligated to Illumina adaptors (final concentration 6.67 nM) that have a T- overhang. USER enzyme was used to cleave the uracil hairpin of the Illumina adaptor, and adaptor-ligated DNA was column purified. The library was PCR amplified for 16-18 cycles using a universal primer and a barcoded primer (New England Biolabs, catalogue #E7335L). PCR-amplified DNA was purified using PCR column purification and eluted in 20 uL of elution buffer for preparation of gel extraction, or 30 uL of TE for preparation of Pippin Prep size selection. Library samples were size selected from 200-350bp using a 2% agarose dye-free automated size selection cassette from Pippin Prep (Sage Sciences, catalogue #CDF2010).

text: Black

characteristic: ethnicity

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: aorta endothelium

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Program in Genetics and Genome Biology, the Hospital for Sick Children, Department of Molecular Genetics, University of Toronto

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: endothelial cell

text: human

text: Caucasian

text: Homo sapiens

text: Homo sapiens

text: aorta endothelium

text: Homo sapiens

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: endothelial cell

text: human

characteristic: description

text: Black

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: aorta endothelium

text: Homo sapiens

text: male

characteristic: title


text: SCAID

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: collection date

text: Mtb isolate from the laboratory animal #16 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 44th day after infection (30th day of the experiment).

text: Kazakhstan

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: human

characteristic: host scientific name

characteristic: isolate

text: sputum

characteristic: isolation source

text: 48.00 N 68.00 E

characteristic: lat lon

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.2.30.16 from MDR-TB infected guinea pig


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SCAID

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Mtb isolate from the laboratory animal #30 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 59th day after infection (45th day of the experiment).

text: Kazakhstan

text: diseased

text: human

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.2.45.30 from MDR-TB infected guinea pig


characteristic: External Id

text: SCAID

characteristic: INSDC center name

text: public

text: Mtb isolate from the laboratory animal #7 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 59th day after infection (45th day of the experiment).

characteristic: description

text: Kazakhstan

text: diseased

text: human

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: Isolate 187.2.45.7 from MDR-TB infected guinea pig


text: SCAID

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Mtb isolate from the laboratory animal #46 infected with MTB-TB M. tuberculosis SCAID 187.0 (CP012506) on 30th day of treatment with antibiotics (44th day after infection).

text: Kazakhstan

text: diseased

text: human

text: sputum

text: 48.00 N 68.00 E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Isolate 187.3.30.46 from MDR-TB infected guinea pig

characteristic: title