text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-63-4


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NCGR

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: rice

characteristic: common name

text: Oryza sativa

characteristic: organism

text: Oryza sativa

text: F2 line HRF3-63-5

characteristic: title

type: has member


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-6-3


text: NCGR

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text: F2 line HRF3-64-1


text: NCGR

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text: NCGR

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text: NCGR

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text: F2 line HRF3-64-4


text: NCGR

text: public

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text: Oryza sativa

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text: NCGR

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text: F2 line HRF3-6-4


text: NCGR

text: public

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text: F2 line HRF3-65-1


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-65-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-65-3


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-65-4


text: NCGR

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text: F2 line HRF3-65-5


text: NCGR

text: public

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text: Oryza sativa

text: F2 line HRF3-6-5


text: NCGR

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text: F2 line HRF3-66-1


text: NCGR

text: public

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text: F2 line HRF3-66-2


text: NCGR

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text: Oryza sativa

text: F2 line HRF3-66-3


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text: F2 line HRF3-66-4


text: NCGR

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text: NCGR

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text: F2 line HRF3-67-1


text: NCGR

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text: F2 line HRF3-67-2


text: NCGR

text: public

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text: Oryza sativa

text: F2 line HRF3-67-3


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text: F2 line HRF3-67-4


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text: NCGR

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text: Oryza sativa

text: F2 line HRF3-68-1


text: NCGR

text: public

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text: Oryza sativa

text: F2 line HRF3-68-2


text: NCGR

text: public

text: rice

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text: F2 line HRF3-68-3


text: NCGR

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text: F2 line HRF3-68-4


text: NCGR

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text: F2 line HRF3-68-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-69-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-69-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-69-3


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-69-4


text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-69-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-70-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-70-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-70-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-70-4


text: NCGR

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text: F2 line HRF3-70-5


text: NCGR

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-71-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-71-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-71-3


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-71-4


text: NCGR

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text: Oryza sativa

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text: F2 line HRF3-71-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-72-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-72-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-72-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-72-4


text: NCGR

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text: Oryza sativa

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text: F2 line HRF3-72-5


text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-7-2


text: NCGR

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text: Oryza sativa

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text: F2 line HRF3-73-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-73-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-73-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-73-4


text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-73-5


text: NCGR

text: public

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text: F2 line HRF3-7-3


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-74-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-74-2


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-74-3


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-74-4


text: NCGR

text: public

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text: F2 line HRF3-74-5


text: NCGR

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text: F2 line HRF3-7-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-75-1


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-75-2


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-75-3


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text: public

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text: Oryza sativa

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text: F2 line HRF3-75-4


text: NCGR

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text: NCGR

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text: F2 line HRF3-7-5


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-76-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-76-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-76-3


text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-76-4


text: NCGR

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text: F2 line HRF3-76-5


text: NCGR

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text: rice

text: Oryza sativa

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text: F2 line HRF3-77-1


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-77-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-77-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-77-4


text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-77-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-78-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-78-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-78-3


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-78-4


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-78-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-79-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-79-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-79-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-79-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-79-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-80-1


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-80-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-80-3


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-80-4


text: NCGR

text: public

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text: Oryza sativa

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text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-81-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-81-2


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-81-3


text: NCGR

text: public

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text: NCGR

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text: NCGR

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text: Oryza sativa

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text: F2 line HRF3-8-1


text: NCGR

text: public

text: rice

text: Oryza sativa

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text: F2 line HRF3-82-1


text: NCGR

text: public

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text: F2 line HRF3-82-2


text: NCGR

text: public

text: rice

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text: NCGR

text: public

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text: NCGR

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text: NCGR

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text: NCGR

text: public

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text: F2 line HRF3-83-1


text: NCGR

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text: NCGR

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text: NCGR

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text: NCGR

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text: NCGR

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text: NCGR

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text: F2 line HRF3-85-1


text: NCGR

text: public

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text: NCGR

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text: NCGR

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text: NCGR

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text: F2 line HRF3-86-1


text: NCGR

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text: F2 line HRF3-86-2


text: NCGR

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text: F2 line HRF3-86-3


text: NCGR

text: public

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text: NCGR

text: public

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text: NCGR

text: public

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text: Oryza sativa

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text: F2 line HRF3-87-1


text: NCGR

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text: NCGR

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text: public

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text: F2 line HRF3-87-4


text: NCGR

text: public

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text: NCGR

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text: F2 line HRF3-88-1


text: NCGR

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text: Oryza sativa

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text: NCGR

text: public

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text: NCGR

text: public

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text: public

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text: NCGR

text: public

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text: public

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text: Oryza sativa

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text: F2 line HRF3-94-1


text: NCGR

text: public

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text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-94-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-94-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-94-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-94-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-9-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-95-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-95-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-95-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-95-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-95-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-9-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-96-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-96-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-96-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-96-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-96-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-97-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-97-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-97-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-97-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-97-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-98-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-98-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-98-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-98-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-98-5


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-99-1


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-99-2


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-99-3


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-99-4


text: NCGR

text: public

text: rice

text: Oryza sativa

text: Oryza sativa

text: F2 line HRF3-99-5


text: ESTONIAN BIOCENTRE, ESTONIA

text: public

tag: Namespace:ESTONIAN BIOCENTRE, ESTONIA

text: human

text: Homo sapiens

text: Homo sapiens

text: human complete genome


text: DTU-GE

text: public

text: DTU-GE

characteristic: broker name

characteristic: collection date

text: Denmark

characteristic: geographic location (country and/or sea)

text: Sus scrofa domesticus

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: No

characteristic: note

text: Staphylococcus aureus

text: Staphylococcus aureus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DTU-GE

text: public

text: DTU-GE

text: Denmark

text: Homo sapiens

text: Yes

text: No

text: Staphylococcus aureus

text: Staphylococcus aureus


text: NORWEGIAN INSTITUTE OF PUBLIC HEALTH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:NORWEGIAN INSTITUTE OF PUBLIC HEALTH

text: Members of an Afghan M. tuberculosis strain family isolated in Norway

characteristic: description

text: Norway

text: diseased

characteristic: host health state

text: Human

text: Human body

characteristic: isolation source

text: 59°57′N 10°45′E

characteristic: lat lon

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: KU LEUVEN - UNIVERSITY OF LEUVEN

text: public

characteristic: SRA accession

tag: Namespace:KU LEUVEN - UNIVERSITY OF LEUVEN

characteristic: Submitter Id

text: human

characteristic: common name

text: The FMR1 gene contains an unstable CGG repeat in its 5’ untranslated region. A repeat with 55-200 CGG units is called a premutation allele and often expands to a full mutation during female germline transmission giving rise to the fragile X syndrome. The risk for a premutation to expand depends on both size and AGG interruptions in the CGG repeat. Unfortunately, the detection of AGG interruptions is hampered by technical difficulties. In order to circumvent the various limitations of TP-PCR, we explored single-molecule sequencing to determine the number and location of AGG interruptions in both males and females carrying FMR premutation alleles. Therefore we first pooled different FMR1 amplicons by using barcodes from PacBio's 96 Barcode design (details can be found in the manuscript) followed by single-molecule sequencing and selection of reads-of-inserts with a minimum of 10 full passes. We demonstrated that single-molecule sequencing enables the determination of not only the repeat size, but also the complete repeat structure including AGG interruptions in male and female alleles with repeats ranging from 45 to 100 CGG units.

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: AGG interruption detection in FMR1 premutation carriers by single-molecule sequencing--run2_repeat

characteristic: title


characteristic: ENA-CHECKLIST

text: NORWEGIAN INSTITUTE OF PUBLIC HEALTH

text: public

characteristic: collection date

text: Norway

characteristic: geographic location (country and/or sea)

text: diseased

text: Human

characteristic: host scientific name

characteristic: isolate

text: Human body

text: 59°57′N 10°45′E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: WGS of Afghan M. tuberculosis strain family members isolated in Norway and Denmark


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NORWEGIAN INSTITUTE OF PUBLIC HEALTH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Denmark

text: diseased

text: Human

text: Human body

text: 55°40′34″N 12°34′06″E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: NORWEGIAN INSTITUTE OF PUBLIC HEALTH

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Norway

text: diseased

characteristic: host health state

text: Human

text: Human body

characteristic: isolation source

text: 55°40′34″N 12°34′06″E

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: KU LEUVEN - UNIVERSITY OF LEUVEN

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Overview of females with their corresponding barcodes included in this run. Please check the corresponding paper to find the FMR genotypes. Male Barcode 1 1 2 17 3 29 4 19 5 9 6 21 7 10 Female Barcode 2 54 2 82 2 75 4 46 12 52 12 70 12 62 17 51 17 55 17 56 31 34 32 35 33 38 34 40

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: AGG interruption detection in FMR1 premutation carriers by single-molecule sequencing--run2


characteristic: ENA-CHECKLIST

text: KU LEUVEN - UNIVERSITY OF LEUVEN

text: public

text: human

text: Overview of females with their corresponding barcodes included in this run. Please check the corresponding paper to find the FMR genotypes. 1 2 2 18 5 5 11 20 12 16 14 17 16 11 17 15 18 19 20 10 21 3 23 13 24 14 27 6

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: AGG interruption detection in FMR1 premutation carriers by single-molecule sequencing--run 1

characteristic: title


text: public

tag: Namespace:Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

text: ArrayExpress

characteristic: broker name

text: thale cress

text: Protocols: Seeds were surface-sterilized and sown in MS-agar medium and stratified at 4°C in darkness for 3 days, then germinated for one week under long days (16h light/8h dark) at 21°C. RNeasy Plant Mini Kit (Qiagen) and DNase I treated (Promega) preparation of strand-specific cDNA libraries: Purification of poly-A containing mRNA molecules; mRNA fragmentation; Random primed cDNA synthesis (strand specific); Adapter ligation and adapter specific PCR amplification.

text: Seedling

characteristic: developmental stage

text: Columbia

characteristic: ecotype

characteristic: genetic modification

text: Arabidopsis thaliana

text: Arabidopsis thaliana

characteristic: replicate

text: Arabidopsis thaliana


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium Department of Plant Systems Biology,VIB, Gent, Belgium

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: thale cress

text: Seedling

text: Columbia

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Arabidopsis thaliana


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: long-grained rice

text: Protocols: The sample material was 12 pooled fourth leaves of individual plants for the control line and the epiline LR2, which belongs to the 4th selfing of the EUE selection pedigree. LR2 and the control line were grown in soil in a growth chamber at 26 C / 21 C (day / night) for 24 days with a 16 h light/8 h dark regime (light intensity was 300 mol m-2 sec-1, the relative humidity was kept at 71%) DNA isolation was performed using the CTAB (cetyltrimethyl/ammonium bromide) standard protocol For WGBS, paired-end bisulfite sequencing libraries were constructed by Alpha Biolaboratory, Inc. Saratoga, CA as described previously (Ibarra et al., 2012) with modifications. About 300 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon, Huntsville, AL) according to the manufacturer’s (Illumina, San Diego, CA) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen, Hilden, Germany) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 µL of 10 x Extaq reaction buffer, 25 µM dNTPs, 1 µL primer 1.1, 1 µl primer 2.1 in a 50 µL reaction. The thermocyling conditions were as follows: 95°C for 3 min, then 12-14 cycles of 95°C for 30 s, 65°C for 30 s and 72°C for 60 s. The enriched libraries were purified twice with solid phase reversible immobilization (SPRI) method using 0.8 x v/v AM-Pure beads (Beckman Coulter, Brea, CA) prior to quantification with a Bioanalyzer (Agilent Technologies, Santa Clara, CA).

text: leaf

characteristic: organims part

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

text: Oryza sativa Indica Group

characteristic: selfing

characteristic: sequencing run

characteristic: strain


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:UNIVERSITY OF BRITISH COLUMBIA, DEPT BOTANY

characteristic: Submitter Id

text: Polynucleobacter necessarius

characteristic: organism

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes aediculatus PPGSP_Eae1

characteristic: title


text: UNIVERSITY OF BRITISH COLUMBIA, DEPT BOTANY

text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes aediculatus PPGSP_Eeae2


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes aediculatus PPGSP_Eae3


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes aediculatus PPGSP_Eae5


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes daidaleos PPGSP_Eda1


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes octocarinatus PPGSP_Eoc1


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes woodruffi PPGSP_Ewo1


text: public

text: Polynucleobacter necessarius

text: Polynucleobacter necessarius

text: Genome sequence of Polynucleobacter harbored by Euplotes harpa Fsp1.4


text: Center of Innovative and bioprocessing

text: public

tag: Namespace:Center of Innovative and bioprocessing

characteristic: collection date

unit: m

characteristic: depth

text: soil

characteristic: environment (biome)

text: Field

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

text: Metagenome sequencing of soil samples

characteristic: project name

text: soil metagenome

text: Illumina

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: Metagenomic samples from soil


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BGI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: common name

text: human gut

text: human-associated habitat

text: faeces

text: China

text: China

text: human-gut

characteristic: human gut environmental package

text: metagenome

text: human gut metagenome

text: ACVD

text: human gut metagenome

text: Illumina

text: Stool sample from China


E-MTAB-5015:1690 dst P2

text: public

text: E-MTAB-5015:1690 dst P2

tag: Namespace:University of Cambridge Department of Paediatrics

characteristic: Submitter Id

unit: year

characteristic: age

text: organoid

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

text: Protocols: Following ethical approval (REC-12/EE/0482) and informed consent, intestinal biopsies were collected from the terminal ileum (TI) and sigmoid colon (SC) from children under 16 years of age undergoing routine diagnostic endoscopy. All children included in this study were found to have macroscopically and histologically entirely normal mucosa as well as no subsequent evidence of any underlying GI pathology. Foetal intestine was obtained with ethical approval (REC-96/085) and informed consent from elective terminations for reasons other than maternal physical health or foetal disease at 8-12 week gestation. Foetal gut was dissected and divided into the proximal (small intestine) and distal (large intestine) sections at the ileo-caecal junction. Mucosal biopsies were washed three times with cold, sterile PBS. For foetal organoids, the dissected small or large intestine was washed and minced with a scalpel blade. Tissues were incubated for 30 min at 4o C on a roller- mixer in 2.5 mM EDTA solution. EDTA was dissolved in either Complete Chelating Solution + Dithiothreitol (5.6 mM Na2HPO4, 8.0 mM K2PO4, 96.2 mM NaCl, 1.6 mM KCl, 43.4 mM Sucrose, 54.9 mM D-Sorbitol, 0.5 mM DTT, all from Sigma, St. Louis, MO, USA) for TI biopsies and foetal gut or dissolved in PBS for SC biopsies. After five washes with cold PBS, intestinal crypts were released by pipetting. Crypt suspension was spun down at 800g for 5 min and resuspended in Matrigel matrix (Sigma, St. Louis, MO, USA). Around 100 crypts were seeded per well in 20 μl of Matrigel (Corning, Corning, NY USA) on a pre-warmed 48-well plate (Corning, Corning, NY USA) and covered with organoid culture medium DNA and RNA were extracted simultaneously from the same sample using Qiagen AllPrep Mini Kit (Qiagen) Illumina TruSeq protocol according to manufacturer's recommendation

characteristic: description

text: fetal stage

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: passage

text: distal gut

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

text: 1690 dst P2

characteristic: title


E-MTAB-5015:1720 dst P7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Cambridge Department of Paediatrics

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5015:1720 dst P7

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: distal gut

text: Homo sapiens

text: male

text: 1720 dst P7


E-MTAB-5015:1769 dst P2

text: public

characteristic: SRA accession

text: E-MTAB-5015:1769 dst P2

characteristic: Submitter Id

characteristic: age

text: organoid

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: distal gut

text: Homo sapiens

text: female

text: 1769 dst P2


E-MTAB-5015:1770 dst P1

text: public

text: E-MTAB-5015:1770 dst P1

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

characteristic: description

text: fetal stage

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: passage

text: distal gut

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: 1770 dst P1


E-MTAB-5015:1780 dst

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5015:1780 dst

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: distal gut

text: Homo sapiens

text: male

text: 1780 dst

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not available

characteristic: age

text: purified cell

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

text: Protocols: Following ethical approval (REC-12/EE/0482) and informed consent, intestinal biopsies were collected from the terminal ileum (TI) and sigmoid colon (SC) from children under 16 years of age undergoing routine diagnostic endoscopy. All children included in this study were found to have macroscopically and histologically entirely normal mucosa as well as no subsequent evidence of any underlying GI pathology. Foetal intestine was obtained with ethical approval (REC-96/085) and informed consent from elective terminations for reasons other than maternal physical health or foetal disease at 8-12 week gestation. Foetal gut was dissected and divided into the proximal (small intestine) and distal (large intestine) sections at the ileo-caecal junction. Purification of intestinal epithelial cells Samples were washed three times in Hank’s Balanced Salt Solution (HBSS), followed by enzyme digestion using a mix of liberase and hyaluronidase in HBSS for 45 min at 37 °C. The cell suspension was passed through a 40 μM sieve, spun down at 1500 rpm at 4 oC for 7 min and re-suspended in phosphate-buffered saline (PBS) containing 10 % bovine serum albumin (BSA) and 100 IU/ml DNase. Cells were then stained with anti-CD326 magnetic microbeads and Fc-Receptor block for 30 min at 4 oC. A magnetic-associated, automated cell separation system (MACS, Miltenyi Biotec) was used to positively select for CD326+ cells. Sorted cells were re-suspended in RLT Plus lysis buffer (Qiagen) supplemented with 1 % β-Mercaptoethanol, passed through a Qiagen shredder column and stored at -80 °C until further processing. Mucosal biopsies were washed three times with cold, sterile PBS. For foetal organoids, the dissected small or large intestine was washed and minced with a scalpel blade. Tissues were incubated for 30 min at 4o C on a roller- mixer in 2.5 mM EDTA solution. EDTA was dissolved in either Complete Chelating Solution + Dithiothreitol (5.6 mM Na2HPO4, 8.0 mM K2PO4, 96.2 mM NaCl, 1.6 mM KCl, 43.4 mM Sucrose, 54.9 mM D-Sorbitol, 0.5 mM DTT, all from Sigma, St. Louis, MO, USA) for TI biopsies and foetal gut or dissolved in PBS for SC biopsies. After five washes with cold PBS, intestinal crypts were released by pipetting. Crypt suspension was spun down at 800g for 5 min and resuspended in Matrigel matrix (Sigma, St. Louis, MO, USA). Around 100 crypts were seeded per well in 20 μl of Matrigel (Corning, Corning, NY USA) on a pre-warmed 48-well plate (Corning, Corning, NY USA) and covered with organoid culture medium DNA and RNA were extracted simultaneously from the same sample using Qiagen AllPrep Mini Kit (Qiagen) Illumina TruSeq protocol according to manufacturer's recommendation

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: distal gut

text: Homo sapiens

text: mixed sex


E-MTAB-5015:1690 px P2

text: public

text: E-MTAB-5015:1690 px P2

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: fetal stage

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: passage

text: proximal gut

text: Homo sapiens

text: female

text: 1690 px P2


E-MTAB-5015:1720 px P7

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5015:1720 px P7

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: proximal gut

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: 1720 px P7


E-MTAB-5015:1769 px P1

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:1769 px P1

characteristic: Submitter Id

characteristic: age

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: proximal gut

text: Homo sapiens

text: female

text: 1769 px P1

characteristic: title


E-MTAB-5015:1770 px P1

text: public

text: E-MTAB-5015:1770 px P1

text: organoid

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: fetal stage

characteristic: developmental stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: proximal gut

text: Homo sapiens

text: male

text: 1770 px P1


E-MTAB-5015:1780 prox P1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-5015:1780 prox P1

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: fetal stage

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: passage

text: proximal gut

text: Homo sapiens

text: male

text: 1780 prox P1


E-MTAB-5015:FPG+ 1792

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:FPG+ 1792

characteristic: Submitter Id

text: purified cell

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: fetal stage

text: Homo sapiens

text: Homo sapiens

text: proximal gut

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: FPG+ 1792


E-MTAB-5015:FPG+ Mg

text: public

text: E-MTAB-5015:FPG+ Mg

text: -0.6 to -0.54

characteristic: age

text: purified cell

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: fetal stage

text: Mg

text: Homo sapiens

text: Homo sapiens

text: proximal gut

text: Homo sapiens

text: female

text: FPG+ Mg

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: purified cell

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: fetal stage

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

text: proximal gut

text: Homo sapiens

text: male


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: not available

text: purified cell

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: fetal stage

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: proximal gut

text: Homo sapiens

text: not available


text: public

characteristic: Submitter Id

characteristic: age

text: purified cell

characteristic: biosource type

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: juvenile stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: purified cell

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: male

characteristic: title


E-MTAB-5015:212 SC P6

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5015:212 SC P6

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: juvenile stage

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

characteristic: passage

text: sigmoid colon

text: Homo sapiens

text: male

text: 212 SC P6


E-MTAB-5015:223 SC P2

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:223 SC P2

characteristic: Submitter Id

characteristic: age

text: organoid

characteristic: biosource type

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: juvenile stage

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: female

text: 223 SC P2


E-MTAB-5015:224 SC P3

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5015:224 SC P3

text: organoid

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

text: juvenile stage

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

text: 224 SC P3


E-MTAB-5015:229 SC P1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5015:229 SC P1

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

characteristic: description

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: sigmoid colon

text: Homo sapiens

text: male

text: 229 SC P1

characteristic: title


E-MTAB-5015:242 SC P1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:242 SC P1

characteristic: Submitter Id

characteristic: age

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: juvenile stage

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

characteristic: passage

text: sigmoid colon

text: Homo sapiens

text: female

text: 242 SC P1


characteristic: ENA-CHECKLIST

text: public

text: purified cell

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

characteristic: cell type

text: human

characteristic: common name

text: juvenile stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: terminal ileum

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: purified cell

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: terminal ileum

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


E-MTAB-5015:212 TI P6

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:212 TI P6

characteristic: Submitter Id

characteristic: age

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

characteristic: description

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: terminal ileum

text: Homo sapiens

text: male

text: 212 TI P6

characteristic: title


E-MTAB-5015:223 TI P2

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5015:223 TI P2

text: organoid

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

text: juvenile stage

characteristic: developmental stage

text: Homo sapiens

text: Homo sapiens

characteristic: passage

text: terminal ileum

text: Homo sapiens

text: female

text: 223 TI P2


E-MTAB-5015:224 TI P2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5015:224 TI P2

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: juvenile stage

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: terminal ileum

text: Homo sapiens

text: female

text: 224 TI P2


E-MTAB-5015:229 TI P1

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5015:229 TI P1

characteristic: Submitter Id

characteristic: age

text: organoid

text: ArrayExpress

text: intestinal epithelial organoid

text: human

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: terminal ileum

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex

text: 229 TI P1


E-MTAB-5015:242 TI P1

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-5015:242 TI P1

text: organoid

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial organoid

characteristic: cell type

text: human

characteristic: common name

characteristic: description

text: juvenile stage

text: Homo sapiens

text: Homo sapiens

text: terminal ileum

text: Homo sapiens

text: female

text: 242 TI P1

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELSINSKI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: Finland

characteristic: geographic location (country and/or sea)

text: healthy

characteristic: host health state

text: Chicken

characteristic: host scientific name

characteristic: isolate

text: feces

characteristic: isolation source

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


BRTI

characteristic: ENA-CHECKLIST

text: HELSINSKI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: BRTI

characteristic: Submitter Id

text: Finland

text: healthy

text: Chicken

text: BRTI

text: feces

text: Campylobacter jejuni

characteristic: organism

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


characteristic: ENA-FIRST-PUBLIC

text: HELSINSKI

text: public

text: Finland

text: healthy

text: chicken

text: feces

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HELSINSKI

text: public

text: Finland

text: healthy

text: Goose

text: feces

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


text: HELSINSKI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Finland

text: healthy

text: Goose

text: Feces

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


text: HELSINSKI

text: public

characteristic: collection date

text: Estonia

characteristic: geographic location (country and/or sea)

text: healthy

text: Chicken

text: meat

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


text: HELSINSKI

text: public

text: Lithuania

text: healthy

characteristic: host health state

text: Chicken

characteristic: host scientific name

text: meat

text: Campylobacter jejuni

text: Campylobacter jejuni

text: Campylobacter jejuni WGS


Inoculum

text: EESC/USP

text: public

text: Inoculum

text: Anaerobic Reactor

characteristic: environment (biome)

text: Anaerobic Reactor

characteristic: environment (feature)

text: Granular Sludge

characteristic: environment (material)

text: Brazil

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: Anaerobic reactor with Fe(III) supplementation

characteristic: project name

text: metagenome

text: IonTorrent

characteristic: sequencing method

text: Inoculum

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


Reactor

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EESC/USP

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Reactor

characteristic: Submitter Id

text: Anaerobic Reactor

text: Anaerobic Reactor

text: Granular Sludge

text: Brazil

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: IonTorrent

characteristic: title

text: wastewater/sludge


characteristic: External Id

text: NTNU

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Latitude End

characteristic: Longitude End

characteristic: depth

text: Incubations of oil accommodated sea-water.

characteristic: description

text: Marine biome

characteristic: environment (biome)

text: Fjord

characteristic: environment (feature)

text: Water

text: water

characteristic: environmental package

text: 2014-07-20T08:00:00Z/2014-07-20T09:00:00Z

characteristic: event date/time

characteristic: latitude start

characteristic: longitude start

text: Norwegian sea

characteristic: marine region

text: marine metagenome

text: PETROMAKS

text: Incubation

characteristic: protocol label

unit: practical salinity unit

characteristic: salinity

characteristic: sampling campaign

text: Underwater pipeline

characteristic: sampling platform

characteristic: sampling site

text: marine metagenome

unit: ºC

characteristic: temperature


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Cancer Research UK Cambridge Institute University of Cambridge

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: The Tc1 mouse line was obtained from Dr. E. Fisher and Dr. V. Tybulewizc and housed in the Biological Resources Unit (BRU) in the Cancer Research UK - Cambridge Institute under the Home Office Licence (PPL 70/7535). For maintenance of the transgenic line, the human chromosome 21 (HsChr21) was transmitted through the female germline by breeding female Tc1 mice to male (129S8 x C57BL/6J) F1 mice (conventional breeding setup). For male germline transmission, female (129S8 x C57BL/6J) F1 mice were crossed with male Tc1 mice. Samples were harvested after direct perfusion of the liver with buffered salt solution and cross-linked in 1% formaldehyde for 20 minutes, followed by quenching with 1/20 volume of 2.5M glycine to neutralise formaldehyde. Cross-linked tissues were homogenised in dounce tissue grinder and lysed according to published protocols (10.1016/j.ymeth.2009.03.001). Sonication was performed on a Misonix sonicator 3000 with a 418 tip to fragment chromatin to an average length of 300bp. 50 ul of cell lysate after sanitation were removed as input control DNA and processed alongside ChIP samples. The following antibodies were used for immuno-precipitation: H3K4me3 (Millipore 05-1339 CMA304, Lot numbers 236661 and 2504863), H3K27ac (abcam ab4729, Lot numbers GR150367 and GR200563), CEBPA (Santa Cruz sc-9314, Lot L1113), HNF4A (ARP31946, Lot numbers QC22894 and QC1455(R1)100317), RNA polymerase II (abcam, ab5408, Lot number GR106949). Immuno-precipitated DNA or 50ng of input DNA was used for library preparation following the standard Illumina TruSeq ChIP Sample preparation protocol.

characteristic: genotype

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

characteristic: organism part

text: Female Germline

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Cambridge Institute University of Cambridge

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: liver

text: Female Germline

text: Mus musculus

text: male


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: liver

text: Male Germline

text: Mus musculus

text: male


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: The Tc1 mouse line was obtained from Dr. E. Fisher and Dr. V. Tybulewizc and housed in the Biological Resources Unit (BRU) in the Cancer Research UK - Cambridge Institute under the Home Office Licence (PPL 70/7535). For maintenance of the transgenic line, the human chromosome 21 (HsChr21) was transmitted through the female germline by breeding female Tc1 mice to male (129S8 x C57BL/6J) F1 mice (conventional breeding setup). For male germline transmission, female (129S8 x C57BL/6J) F1 mice were crossed with male Tc1 mice. Samples were harvested after direct perfusion of the liver with buffered salt solution and cross-linked in 1% formaldehyde for 20 minutes, followed by quenching with 1/20 volume of 2.5M glycine to neutralise formaldehyde. Cross-linked tissues were homogenised in dounce tissue grinder and lysed according to published protocols (10.1016/j.ymeth.2009.03.001). Sonication was performed on a Misonix sonicator 3000 with a 418 tip to fragment chromatin to an average length of 300bp. 50 ul of cell lysate after sanitation were removed as input control DNA and processed alongside ChIP samples. The following antibodies were used for immuno-precipitation: H3K4me3 (Millipore 05-1339 CMA304, Lot numbers 236661 and 2504863), H3K27ac (abcam ab4729, Lot numbers GR150367 and GR200563), CEBPA (Santa Cruz sc-9314, Lot L1113), HNF4A (ARP31946, Lot numbers QC22894 and QC1455(R1)100317), RNA polymerase II (abcam, ab5408, Lot number GR106949). Up to 50ng of immuno-precipitated DNA or input DNA was used for library preparation following the ThruPLEX DNA-Seq library preparation protocol.

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: liver

text: Male Germline

text: Mus musculus

text: male


text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

characteristic: organism

text: Mus musculus

text: brain

characteristic: organism part

text: Female Germline

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: kidney

text: Female Germline

text: Mus musculus

text: male

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: muscle

text: Female Germline

text: Mus musculus

text: male


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: brain

text: Male Germline

text: Mus musculus

text: male


text: public

text: ArrayExpress

text: house mouse

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: kidney

characteristic: organism part

text: Male Germline

characteristic: phenotype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: muscle

text: Male Germline

text: Mus musculus

text: male

characteristic: strain


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: liver

text: Female Germline

text: Mus musculus

text: male

characteristic: title


Pseudomonas chlororaphis FW305-25

text: OAK RIDGE NATIONAL LABORATORY

text: public

characteristic: SRA accession

text: Pseudomonas chlororaphis FW305-25

tag: Namespace:OAK RIDGE NATIONAL LABORATORY

characteristic: Submitter Id

text: Pseudomonas chlororaphis

text: Pseudomonas chlororaphis

text: Pseudomonas chlororaphis FW305-25


text: IPF

text: public

text: Peronospora belbahrii

text: Peronospora belbahrii

text: Peronospora belbahrii genome analyses


APytT

text: public

text: APytT

tag: Namespace:WAGENINGEN UNIVERSITY, LABORATORY OF SYSTEMS AND SYNTHETIC BIOLOGY.

text: Akkermansia glycaniphila strain PytT

characteristic: description

text: Akkermansia glycaniphila

text: Akkermansia glycaniphila

text: Akkermansia glycaniphila strain PytT


PYXNL

text: KAUST

text: public

text: PYXNL

text: Plasmodium yoelii yoelii

characteristic: organism

text: Plasmodium yoelii yoelii

text: Total RNA from Plasmodium yoelii strains


text: KAUST

text: public

text: Plasmodium yoelii yoelii

text: Plasmodium yoelii yoelii


PYCU

text: KAUST

text: public

text: PYCU

text: Plasmodium yoelii yoelii

text: Plasmodium yoelii yoelii


PYCUCdY

text: KAUST

text: public

text: PYCUCdY

text: Plasmodium yoelii yoelii

text: Plasmodium yoelii yoelii


text: EMBL

text: public

text: house mouse

characteristic: common name

text: WT

text: Mus musculus

text: Mus musculus

text: cortical thymic epithelial cells


text: EMBL

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: cortical thymic epithelial cells


text: EMBL

text: public

text: house mouse

text: WT

text: Mus musculus

text: Mus musculus

text: medullary thymic epithelial cells


text: EMBL

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: medullary thymic epithelial cells


text: UNIVERSITY OF LIVERPOOL

text: public

tag: Namespace:UNIVERSITY OF LIVERPOOL

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

characteristic: lab host

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Replicate 1


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Replicate 2


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Replicate 3


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Replicate 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Replicate 5


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Staphylococcus aureus subsp. aureus MSSA476

text: Replicate 1


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Replicate 2


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Replicate 3


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Replicate 4


text: UNIVERSITY OF LIVERPOOL

text: public

text: 5th generation

text: Caenorhabditis elegans N2 wild-type

text: Replicate 5


text: UNIVERSITY OF LIVERPOOL

text: public

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF

text: Enterococcus faecalis OG1RF experiment ancestral strain


text: UNIVERSITY OF LIVERPOOL

text: public

text: Staphylococcus aureus MSSA476 experiment ancestral strain


E-MTAB-5032:KO1 GLUT1-high

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:KO1 GLUT1-high

tag: Namespace:VIB - KULEUVEN

text: ArrayExpress

characteristic: broker name

text: CD11b+ F4/80+ macrophage

characteristic: cell type

text: house mouse

text: Protocols: LLC tumor-bearing mice were sacrificed by cervical dislocation and tumors were harvested. Tumors were minced in RPMI medium containing 0.1% collagenase type I and 0.2% dispase type I and incubated in the same solution for 30 minutes at 37°C. The digested tissue was filtered using a 70 μm pore sized mesh and cells were centrifuged 5 min at 1000 rpm. Red blood cell lysis was performed by using Hybri-MaxTM (Sigma-Aldrich). For flow sorting, the myeloid cell population in the tumor single cell suspension was enriched by coating with CD11b-conjugated magnetic beads (MACS, Miltenyi Biotec) and separation through magnetic columns (MACS, Miltenyi Biotec). Cells were resuspended in FACS buffer (PBS containing 2% FBS and 2 mM EDTA) and incubated for 15 minutes with Mouse BD Fc Block™ purified anti-mouse CD16/CD32 mAb (BD-pharmingen) and stained with the following antibodies for 20 minutes at 4 °C: anti-F4/80 and anti-GLUT1. Cells were subsequently washed and resuspended in cold FACS buffer before flow sorting by a FACS Aria (BD Biosciences). REDD1 KO mice were generated by Lexicon Corp (USA) exclusively for Quark Pharmaceuticals Inc and are the property of Quark Pharmaceuticals Inc. WT mice were littermate controls. 5-6 weeks old C57BL/6N recipient mice were irradiated with 9.5 Gy. Subsequently, 107 bone marrow cells from the appropriate genotype were injected intravenously via the tail vein. Tumor experiments were initiated 5 weeks after bone marrow reconstitution. : 1 x 106 Lewis lung carcinoma (LLC) adherent growing murine cells were injected subcutaneously at the right side of the mouse in a volume of 200 μl of PBS. Animals were killed 3 weeks after tumor cell injection, and the tumors were processed for FACS sorting immediately. RNeasy microkit from Qiagen RNA concentration and purity from freshly sorted TAMs were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyzer 2100 (Agilent). Per sample, an amount of 100 ng of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version 15031047 Rev.E) poly-A containing mRNA molecules were purified from the total RNA input using poly-T oligo-attached magnetic beads. In a reverse transcription reaction using random primers, RNA was converted into first strand cDNA and subsequently converted into double-stranded cDNA in a second strand cDNA synthesis reaction using DNA Polymerase I and RNAse H. The cDNA fragments were extended with a single ‘A’ base to the 3’ ends of the blunt-ended cDNA fragments after which multiple indexing adapters were ligated introducing different barcodes for each sample. Finally an enrichment PCR of 15 cycles was carried out to enrich those DNA fragments that have adapter molecules on both ends and to amplify the amount of DNA in the library.

text: Lewis lung carcinoma

characteristic: disease

text: Ddit4 knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

characteristic: phenotype

text: Mus musculus

text: KO1 GLUT1-high


E-MTAB-5032:KO1 GLUT1-low

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:KO1 GLUT1-low

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

characteristic: strain

text: KO1 GLUT1-low


E-MTAB-5032:KO2 GLUT1-high

text: VIB - KULEUVEN

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5032:KO2 GLUT1-high

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

text: KO2 GLUT1-high

characteristic: title


E-MTAB-5032:KO2 GLUT1-low

text: VIB - KULEUVEN

text: public

characteristic: SRA accession

text: E-MTAB-5032:KO2 GLUT1-low

characteristic: Submitter Id

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

characteristic: organism

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

text: KO2 GLUT1-low


E-MTAB-5032:KO3 GLUT1-high

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text: public

text: E-MTAB-5032:KO3 GLUT1-high

text: ArrayExpress

characteristic: broker name

text: CD11b+ F4/80+ macrophage

characteristic: cell type

text: house mouse

text: Lewis lung carcinoma

characteristic: disease

text: Ddit4 knockout

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

text: KO3 GLUT1-high


E-MTAB-5032:KO3 GLUT1-low

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:KO3 GLUT1-low

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

characteristic: phenotype

text: Mus musculus

text: KO3 GLUT1-low


E-MTAB-5032:KO4 GLUT1-high

characteristic: External Id

text: VIB - KULEUVEN

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5032:KO4 GLUT1-high

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

characteristic: strain

text: KO4 GLUT1-high


E-MTAB-5032:KO4 GLUT1-low

text: VIB - KULEUVEN

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5032:KO4 GLUT1-low

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: Ddit4 knockout

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

text: KO4 GLUT1-low

characteristic: title


E-MTAB-5032:WT1 GLUT1-high

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT1 GLUT1-high

characteristic: Submitter Id

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

text: WT1 GLUT1-high


E-MTAB-5032:WT1 GLUT1-low

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT1 GLUT1-low

text: ArrayExpress

characteristic: broker name

text: CD11b+ F4/80+ macrophage

characteristic: cell type

text: house mouse

text: Lewis lung carcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

text: WT1 GLUT1-low


E-MTAB-5032:WT2 GLUT1-high

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT2 GLUT1-high

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

characteristic: phenotype

text: Mus musculus

text: WT2 GLUT1-high


E-MTAB-5032:WT2 GLUT1-low

characteristic: External Id

text: VIB - KULEUVEN

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5032:WT2 GLUT1-low

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

characteristic: strain

text: WT2 GLUT1-low


E-MTAB-5032:WT3 GLUT1-high

text: VIB - KULEUVEN

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-5032:WT3 GLUT1-high

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

text: WT3 GLUT1-high

characteristic: title


E-MTAB-5032:WT3 GLUT1-low

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT3 GLUT1-low

characteristic: Submitter Id

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

characteristic: common name

characteristic: description

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: low GLUT1 expression

text: Mus musculus

text: WT3 GLUT1-low


E-MTAB-5032:WT4 GLUT1-high

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT4 GLUT1-high

text: ArrayExpress

characteristic: broker name

text: CD11b+ F4/80+ macrophage

characteristic: cell type

text: house mouse

text: Lewis lung carcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

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text: Mus musculus

text: high GLUT1 expression

text: Mus musculus

text: WT4 GLUT1-high


E-MTAB-5032:WT4 GLUT1-low

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: VIB - KULEUVEN

text: public

text: E-MTAB-5032:WT4 GLUT1-low

text: ArrayExpress

text: CD11b+ F4/80+ macrophage

text: house mouse

text: Lewis lung carcinoma

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: low GLUT1 expression

characteristic: phenotype

text: Mus musculus

text: WT4 GLUT1-low


characteristic: External Id

text: IOA

characteristic: INSDC center name

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text: public

text: European seabass

text: Dicentrarchus labrax

text: Dicentrarchus labrax


text: Michigan State University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Michigan State University

characteristic: collection date

text: human

text: Male.Ears.Thawed

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characteristic: environment (biome)

text: Residental

characteristic: environment (feature)

text: human

characteristic: environment (material)

text: USA

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characteristic: geographic location (longitude)

text: human-associated

characteristic: human associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Homo sapiens

text: Human Postmortem Microbiome

characteristic: project name

text: Homo sapiens

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characteristic: sequencing method

text: Postmortem Microbiome Pediatric Thaw


characteristic: ENA-CHECKLIST

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text: Michigan State University

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characteristic: ENA-CHECKLIST

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