text: CTGTCTATACTA

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

characteristic: Region

text: Root

text: Kito

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: GTGYCAGCMGCCGCGGTAA

text: GGACTACHVGGGTWTCTAAT

text: root metagenome

text: Bacteria


status: PUBLIC

tag: attribute

text: TATGCCAGAGAT

text: TCTCTTTCGACA

text: Control

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Control

text: Control

text: Graz University of Technology

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: control sample

characteristic: Latitude

text: control sample

characteristic: Longitude

text: Control

text: Control

characteristic: SRA accession

text: Control

text: Control

text: Control

text: Control

characteristic: Submitter Id

text: Control

text: Control

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: GTGYCAGCMGCCGCGGTAA

characteristic: primerFwd-pad

text: GGACTACHVGGGTWTCTAAT

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Bacteria

characteristic: target

characteristic: title


text: CATATAGCCCGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Rhizosphere

text: Kabuye

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: GCCTATGAGATC

text: GTAGTAGACCAT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Rhizosphere

text: Kabuye

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CAAGTGAAGGGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Rhizosphere

text: Kabuye

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CACGTTTATTCC

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

characteristic: Submitter Id

text: Kabuye

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TAATCGGTGCCA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

text: Kabuye

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: TGACTAATGGCC

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Rhizosphere

text: Kabuye

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CGGGACACCCGA

text: GTAGTAGACCAT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Rhizosphere

text: Kabuye

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CTGTCTATACTA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Rhizosphere

text: Kabuye

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TATGCCAGAGAT

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

characteristic: Submitter Id

text: Kitwanga

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CGTTTGGAATGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

text: Kitwanga

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: AAGAACTCATGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Rhizosphere

text: Kitwanga

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TGATATCGTCTT

text: GTAGTAGACCAT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Rhizosphere

text: Kitwanga

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CGGTGACCTACT

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Rhizosphere

text: Kitwanga

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: AATGCGCGTATA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

characteristic: Submitter Id

text: Kitwanga

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CTTGATTCTTGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

text: Kitwanga

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: GAAATCTTGAAG

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Rhizosphere

text: Kitwanga

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: GAGATACAGTTC

text: GTAGTAGACCAT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Rhizosphere

text: Kisorosoro

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: GTGGAGTCTCAT

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Rhizosphere

text: Kisorosoro

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: ACCTTACACCTT

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

characteristic: Submitter Id

text: Kisorosoro

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TAATCTCGCCGG

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

text: Kisorosoro

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: ATCTAGTGGCAA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Rhizosphere

text: Kisorosoro

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: ACGCTTAACGAC

text: GTAGTAGACCAT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Rhizosphere

text: Kisorosoro

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TACGGATTATGG

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Rhizosphere

text: Kisorosoro

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: ATACATGCAAGA

text: GTAGTAGACCAT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Rhizosphere

characteristic: Submitter Id

text: Kisorosoro

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CATATAGCCCGA

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Rhizosphere

text: Kagogo

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: GCCTATGAGATC

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

characteristic: Region

text: Rhizosphere

text: Kagogo

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CAAGTGAAGGGA

text: AGTAAAGATCGT

text: Bunyangabu

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Western

text: Rhizosphere

text: Kagogo

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CACGTTTATTCC

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Western

characteristic: SRA accession

text: Rhizosphere

text: Kagogo

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TAATCGGTGCCA

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Rhizosphere

characteristic: Submitter Id

text: Kagogo

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TGACTAATGGCC

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Rhizosphere

text: Kagogo

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: CGGGACACCCGA

text: AGTAAAGATCGT

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

characteristic: Region

text: Rhizosphere

text: Kagogo

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CTGTCTATACTA

text: AGTAAAGATCGT

text: Bunyangabu

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Western

text: Rhizosphere

text: Kagogo

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: TATGCCAGAGAT

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Central

characteristic: SRA accession

text: Rhizosphere

text: Kito

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CGTTTGGAATGA

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Rhizosphere

characteristic: Submitter Id

text: Kito

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: AAGAACTCATGA

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Rhizosphere

text: Kito

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: TGATATCGTCTT

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

text: Central

characteristic: Region

text: Rhizosphere

text: Kito

characteristic: Village

characteristic: collection date

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CGGTGACCTACT

text: AGTAAAGATCGT

text: Mukono

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Central

text: Rhizosphere

text: Kito

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: AATGCGCGTATA

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Central

characteristic: SRA accession

text: Rhizosphere

text: Kito

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: CTTGATTCTTGA

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Rhizosphere

characteristic: Submitter Id

text: Kito

text: Rhizosphere

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


text: GAAATCTTGAAG

text: AGTAAAGATCGT

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Rhizosphere

text: Kito

text: Rhizosphere

text: metagenome

text: Uganda

text: rhizosphere metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: rhizosphere metagenome

text: Fungi

characteristic: target

characteristic: title


text: GAGATACAGTTC

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Root

text: Kabuye

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: GTGGAGTCTCAT

text: AGTAAAGATCGT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Root

text: Kabuye

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ACCTTACACCTT

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Root

text: Kabuye

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TAATCTCGCCGG

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

characteristic: Submitter Id

text: Kabuye

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ATCTAGTGGCAA

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

text: Kabuye

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: ACGCTTAACGAC

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Root

text: Kabuye

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TACGGATTATGG

text: AGTAAAGATCGT

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Root

text: Kabuye

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ATACATGCAAGA

text: AGTAAAGATCGT

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Root

text: Kabuye

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CATATAGCCCGA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

characteristic: Submitter Id

text: Kitwanga

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: GCCTATGAGATC

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

text: Kitwanga

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: CAAGTGAAGGGA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Root

text: Kitwanga

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CACGTTTATTCC

text: CTCGCCCTCGCC

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Root

text: Kitwanga

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

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text: TAATCGGTGCCA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Root

text: Kitwanga

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TGACTAATGGCC

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

characteristic: Submitter Id

text: Kitwanga

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CGGGACACCCGA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

text: Kitwanga

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: CTGTCTATACTA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Root

text: Kitwanga

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

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text: TATGCCAGAGAT

text: CTCGCCCTCGCC

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Root

text: Kisorosoro

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

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text: CGTTTGGAATGA

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text: Kiryandongo

text: Graz University of Technology

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characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Root

text: Kisorosoro

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: AAGAACTCATGA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

characteristic: Submitter Id

text: Kisorosoro

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TGATATCGTCTT

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

text: Kisorosoro

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

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characteristic: target

characteristic: title


text: CGGTGACCTACT

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: Region

text: Root

text: Kisorosoro

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: AATGCGCGTATA

text: CTCGCCCTCGCC

text: Kiryandongo

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Root

text: Kisorosoro

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CTTGATTCTTGA

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

characteristic: SRA accession

text: Root

text: Kisorosoro

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: GAAATCTTGAAG

text: CTCGCCCTCGCC

text: Kiryandongo

text: Graz University of Technology

text: public

text: Root

characteristic: Submitter Id

text: Kisorosoro

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: GAGATACAGTTC

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Root

text: Kagogo

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: GTGGAGTCTCAT

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

characteristic: Region

text: Root

text: Kagogo

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

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characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ACCTTACACCTT

text: CTCGCCCTCGCC

text: Bunyangabu

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Western

text: Root

text: Kagogo

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TAATCTCGCCGG

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Western

characteristic: SRA accession

text: Root

text: Kagogo

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ATCTAGTGGCAA

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Root

characteristic: Submitter Id

text: Kagogo

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ACGCTTAACGAC

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

text: Root

text: Kagogo

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: TACGGATTATGG

text: CTCGCCCTCGCC

text: Bunyangabu

text: Graz University of Technology

text: public

text: Western

characteristic: Region

text: Root

text: Kagogo

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

text: root metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: ATACATGCAAGA

text: CTCGCCCTCGCC

text: Bunyangabu

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Western

text: Root

text: Kagogo

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CATATAGCCCGA

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Central

characteristic: SRA accession

text: Root

text: Kito

text: Root

text: metagenome

text: Uganda

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text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: GCCTATGAGATC

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Root

characteristic: Submitter Id

text: Kito

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CAAGTGAAGGGA

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Root

text: Kito

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: CACGTTTATTCC

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

characteristic: Region

text: Root

text: Kito

characteristic: Village

characteristic: collection date

text: Root

text: metagenome

text: Uganda

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characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TAATCGGTGCCA

text: TCTCTTTCGACA

text: Mukono

characteristic: District

characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: Graz University of Technology

characteristic: INSDC center name

text: public

text: Central

text: Root

text: Kito

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: TGACTAATGGCC

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

characteristic: INSDC status

characteristic: Latitude

characteristic: Longitude

text: Central

characteristic: SRA accession

text: Root

text: Kito

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CGGGACACCCGA

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Root

characteristic: Submitter Id

text: Kito

text: Root

characteristic: common name

text: metagenome

characteristic: description

text: Uganda

characteristic: geographic location (country and/or sea)

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: root metagenome

text: Fungi


text: CTGTCTATACTA

text: TCTCTTTCGACA

text: Mukono

text: Graz University of Technology

text: public

text: Central

text: Root

text: Kito

text: Root

text: metagenome

text: Uganda

text: root metagenome

text: CTTGGTCATTTAGAGGAAGTAA

characteristic: primerFwd-pad

text: GCTGCGTTCTTCATCGATGC

characteristic: primerRev-pad

text: root metagenome

text: Fungi

characteristic: target

characteristic: title


text: TATGCCAGAGAT

text: TCTCTTTCGACA

text: Control

text: Control

text: Control

text: Graz University of Technology

text: public

text: Control

text: Control

text: Control

text: Control

characteristic: Region

text: Control

text: Control

text: Control

text: Control

text: Control

characteristic: Village

characteristic: collection date

text: Control

text: metagenome

text: Uganda

text: rhizosphere metagenome

characteristic: organism

text: CTTGGTCATTTAGAGGAAGTAA

text: GCTGCGTTCTTCATCGATGC

text: rhizosphere metagenome

text: Fungi


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

tag: Namespace:Institute of Clinical Molecular Biology (IKMB)

text: human

text: Tooth from Grave 5 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: Institute of Clinical Molecular Biology (IKMB)

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Tooth from Grave 7 from the Lauchheim burial site in Germany

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 22 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: public

text: human

text: Petrous bone from Grave 22 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 23 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 24 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 24 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 37 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 37 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 56 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 56 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 63 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 67 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 67 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 69 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 70 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 70 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: Institute of Clinical Molecular Biology (IKMB)

text: public

text: human

text: Tooth from Grave 82 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 86 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 78 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 31 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 31 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 16 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 16 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 27 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 29 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 46 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Skull fragment from Grave 46 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Petrous bone from Grave 66 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 66 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 79 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Sternuml fragment from Grave 79 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: public

text: human

text: Tooth from Grave 83 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


text: Institute of Clinical Molecular Biology (IKMB)

text: public

text: human

text: Petrous bone from Grave 83 from the Lauchheim burial site in Germany

text: Homo sapiens

text: Homo sapiens


SAMI00000006-TEST SAMPLE VM4

text: KLE TEch

text: public

text: SAMI00000006-TEST SAMPLE VM4

tag: Namespace:KLE TEch

text: TEST Inst

characteristic: collecting institution

text: TEST Collector

characteristic: collector name

text: TEST DESC

text: Howland Island

characteristic: geographic location (country and/or sea)

text: Corona

characteristic: host common name

text: diseased

characteristic: host health state

text: Homo Sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

text: betacoronavirus

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: TEST SAMPLE VM4


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

tag: Namespace:Division of Immunity, Inflammation and Infection John Curtin School of Medical Research The Australian National University 131 Garran Road Acton, ACT, 2601 AUSTRALIA

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: precursor B cells

text: house mouse

text: Protocols: Single cell suspensions generated from BM were stained with antibodies against CD19, IgM, CD43 and B220. Dead cells were stained by addition of 7AAD. For each sample, 50 Pro B cells were sorted into 4 wells of a 96 well plate (200 cells in total per sample) based on 7AAD-,CD43+IgM-CD19+B220+. In addition, from mutant mice 7AAD-,CD43+CD24+IgM-CD19+B220- cells were also sorted. RNA was extracted using a modified version of the SMARTseq2 protocol from Picelli et al., 2014. 50 Cells were sorted into 96 well plates (4 wells per sample) containing 1ul of the cell lysis buffer, 0.5mL dNTP mix (10mM) and 0.5mL of the oligo dT primer at 5mM. We then reduced the amount of reagent used in the following reverse transcription and PCR amplification step by half. The concentration of the IS PCR primer was also further reduced to 50nM. Due to the low transcriptional activity of resting B cells, we increased the number of PCR cycles to 28. Sequencing libraries were prepared using the Nextera XT Library Preparation Kit with the protocol modified by reducing the original volumes of all reagents in the kit by 1/5th.

text: adult

characteristic: developmental stage

text: PAX5 Y351*/Y351*

characteristic: genotype

characteristic: immunophenotype

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Division of Immunity, Inflammation and Infection John Curtin School of Medical Research The Australian National University 131 Garran Road Acton, ACT, 2601 AUSTRALIA

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: pro-B cell

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: PAX5 Y351*/Y351*

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: female

characteristic: title


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: age

text: ArrayExpress

text: precursor B cells

text: house mouse

text: adult

text: PAX5 Y351*/Y351*

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: female


text: public

text: ArrayExpress

characteristic: broker name

text: pro-B cell

text: house mouse

text: adult

characteristic: developmental stage

text: wild-type genotype

characteristic: genotype

characteristic: immunophenotype

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

text: female


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: University Medical Center Hamburg-Eppendorf

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

text: Protocols: Bone marrow-derived macrophages (BMDMs) were seeded into a 6-well plate at a concentration of 1.2·106 cells/well and exposed to apoptotic cells (apoptotic 6neutrophils (aN), apoptotic thymocytes (aT) and apoptotic hepatocytes (aH)) followed by IL-4 stimulation for 24h as described above (see polarisation assay). BMDMs were collected using cold PBS and 1 Mio cells were inoculated intravenously (i.v.) at week 6 and 7 post infection (p.i.). PBS was used as vehicle control. For the transfer experiments performed during thioglycollate-induced peritonitis, BMDMs were treated with the different apoptotic cells and IL-4, as described above, and transferred intra peritoneally (i.p.) 2 days after thioglycollate injection. PBS was used as vehicle control. BGISEQ-500 Transcriptome library was prepared according to the manufacturer’s protocol. performed by BGI TECH SOLUTIONS, Hongkong

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: apoptotic hepatocytes

characteristic: stimulus

characteristic: strain

text: Mo-aH


characteristic: INSDC center name

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: macrophage

text: not collected

text: house mouse

characteristic: description

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: apoptotic hepatocytes - IL4

characteristic: title


text: public

text: ArrayExpress

text: macrophage

text: not collected

text: house mouse

text: not collected

characteristic: individual

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: Mus musculus

text: apoptotic 6neutrophils

text: Mo-aN


characteristic: ENA first public

text: public

text: ArrayExpress

text: macrophage

text: not collected

text: house mouse

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

text: apoptotic 6neutrophils - IL4


characteristic: ENA-CHECKLIST

text: public

characteristic: SRA accession

text: ArrayExpress

text: macrophage

text: not collected

text: house mouse

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: apoptotic thymocytes

text: Mo-aT


text: public

characteristic: Submitter Id

text: ArrayExpress

text: macrophage

text: not collected

characteristic: collection date

text: house mouse

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: apoptotic thymocytes - IL4


text: public

text: ArrayExpress

text: macrophage

text: not collected

text: house mouse

characteristic: common name

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus


text: public

text: ArrayExpress

text: macrophage

text: not collected

text: house mouse

text: not collected

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: control

characteristic: stimulus

text: Mo-untreated


text: IMSRL (Irish Meningitis and Sepsis Reference Laboratory

characteristic: INSDC center name

text: public

text: Ireland

text: restricted access

characteristic: host health state

text: homo sapiens

characteristic: host scientific name

text: GBS

text: human

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: public

characteristic: INSDC status

text: Ireland

text: restricted access

text: homo sapiens

text: GBS

text: human

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: public

text: Ireland

text: restricted access

text: homo sapiens

text: SPN

text: human

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: title


text: public

text: Ireland

text: restricted access

text: homo sapiens

text: SPN

text: human

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


Blood

text: ICR

text: public

text: Blood

text: human

text: FUME-TCRseq of blood sample

characteristic: description

text: United Kingdom

text: Homo sapiens

text: Homo sapiens

text: Blood


text: Before

characteristic: Exposure

text: Scripps Institution of Oceanography

text: public

text: Pacific oyster

unit: days

text: oyster tissue before OsHV1 exposure

text: before

text: Host-associated

text: Host-associated (saline)

text: Animal corpus (saline)

text: Animal corpus (saline)

text: oyster body

text: USA

unit: copies

text: Crassostrea gigas

characteristic: organism

unit: grams

text: UCSD:SIO

text: D/RNA shield

text: Crassostrea gigas

text: whole oyster tissue


characteristic: ENA first public

text: After

text: Scripps Institution of Oceanography

text: public

text: Pacific oyster

text: dead oyster tissue after OsHV1 exposure

text: dead

text: Host-associated

text: Host-associated (saline)

text: Animal corpus (saline)

text: Animal corpus (saline)

text: oyster body

text: USA

text: Crassostrea gigas

text: UCSD:SIO

text: D/RNA shield

text: Crassostrea gigas

text: whole oyster tissue


characteristic: ENA-CHECKLIST

text: After

text: Scripps Institution of Oceanography

text: public

text: Pacific oyster

text: tissue from oyster with OsHV1 symptoms

text: sick

text: Host-associated

text: Host-associated (saline)

text: Animal corpus (saline)

text: Animal corpus (saline)

text: oyster body

text: USA

text: Crassostrea gigas

text: UCSD:SIO

text: D/RNA shield

text: Crassostrea gigas

text: whole oyster tissue


text: GMU

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:864-22345

characteristic: broad-scale environmental context

text: fecal sample

characteristic: environmental medium

text: China

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

characteristic: project name

text: rat gut metagenome

text: rat gut microbiota sample 1


text: GMU

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:864-22346

characteristic: Submitter Id

characteristic: collection date

text: fecal sample

text: China

characteristic: geographic location (country and/or sea)

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 2


text: GMU

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:864-22347

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 3

characteristic: title


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:864-22348

text: fecal sample

characteristic: description

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 4


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:864-22349

text: fecal sample

text: China

text: rat gut metagenome

characteristic: organism

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 5


characteristic: ENA first public

text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22350

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 6


characteristic: ENA-CHECKLIST

text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22351

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 7


text: GMU

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22352

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 8


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22353

characteristic: broad-scale environmental context

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 9


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22354

text: fecal sample

characteristic: environmental medium

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 10


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22355

text: fecal sample

text: China

characteristic: geographic location (latitude)

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 11


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22356

text: fecal sample

text: China

characteristic: geographic location (longitude)

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 12


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22357

text: fecal sample

text: China

characteristic: local environmental context

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 13


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22358

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

characteristic: project name

text: rat gut metagenome

text: rat gut microbiota sample 14


text: GMU

characteristic: INSDC center name

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22359

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 15


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22360

characteristic: Submitter Id

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 16


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:865-22361

characteristic: collection date

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 17


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22362

text: fecal sample

text: China

characteristic: geographic location (country and/or sea)

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 18


text: GMU

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22363

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 19


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22364

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 20

characteristic: title


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22365

text: fecal sample

characteristic: description

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 21


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22366

text: fecal sample

text: China

text: rat gut metagenome

characteristic: organism

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 22


characteristic: ENA first public

text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22367

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 23


characteristic: ENA-CHECKLIST

text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22368

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 24


text: GMU

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22369

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 25


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22370

characteristic: broad-scale environmental context

text: fecal sample

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 26


text: GMU

text: public

text: ena-SAMPLE-TAB-16-02-2024-16:02:53:866-22371

text: fecal sample

characteristic: environmental medium

text: China

text: rat gut metagenome

text: 16sRNA of rat gut microbiota

text: rat gut metagenome

text: rat gut microbiota sample 27


text: QMUL

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: Hottentot golden mole

characteristic: common name

text: Protocols: Heart was dissected and within 60 seconds placed in cryovial containing RNA later, and flash frozen in liquid nitrogen. Subsequently, samples were placed in the -80C freezer for storage. Total RNA extraction and analysis was performed commercially by BGI Tech solutions (Hong Kong). Oligo dT beads were used to enrich mRNA with a poly A tail. RNA fragmentation and first- strand cDNAs were generated using random N6-primed reverse transcription, followed by the second- strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments. PCR amplification was performed to enrich the purified cDNA template.

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Amblysomus hottentotus

text: Amblysomus hottentotus

text: heart

characteristic: organism part

text: Amblysomus hottentotus

text: female

characteristic: sex


text: QMUL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: house mouse

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: male


characteristic: ENA first public

characteristic: ENA-CHECKLIST

text: QMUL

text: public

text: ArrayExpress

text: not collected

text: Cape dune mole-rat

characteristic: description

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Bathyergus suillus

characteristic: organism

text: Bathyergus suillus

text: heart

text: Bathyergus suillus

text: female

characteristic: title


text: QMUL

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: not collected

text: Cape dune mole-rat

characteristic: common name

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Bathyergus suillus

text: Bathyergus suillus

text: heart

text: Bathyergus suillus

text: male


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

text: Cryptomys hottentotus hottentotus

text: Cryptomys hottentotus hottentotus

text: heart

text: Cryptomys hottentotus hottentotus

text: male


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: CHHA

text: not applicable

characteristic: isolate

text: Cryptomys hottentotus hottentotus

text: Cryptomys hottentotus hottentotus

text: heart

characteristic: organism part

text: Cryptomys hottentotus hottentotus

text: male

characteristic: sex

text: CHHA


text: QMUL

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: CHHB

text: not applicable

text: Cryptomys hottentotus hottentotus

text: Cryptomys hottentotus hottentotus

text: heart

text: Cryptomys hottentotus hottentotus

text: male

text: CHHB


characteristic: ENA first public

text: QMUL

text: public

text: ArrayExpress

text: not collected

characteristic: collection date

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: CHHD

text: not applicable

text: Cryptomys hottentotus hottentotus

text: Cryptomys hottentotus hottentotus

text: heart

text: Cryptomys hottentotus hottentotus

text: male

text: CHHD


characteristic: ENA-CHECKLIST

text: QMUL

text: public

text: ArrayExpress

text: not collected

characteristic: description

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Cryptomys hottentotus mahali

characteristic: organism

text: Cryptomys hottentotus mahali

text: heart

text: Cryptomys hottentotus mahali

text: female


text: QMUL

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: not collected

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Cryptomys hottentotus natalensis

text: Cryptomys hottentotus natalensis

text: heart

text: Cryptomys hottentotus natalensis

text: male

characteristic: title


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

text: not applicable

text: Cryptomys hottentotus natalensis

text: Cryptomys hottentotus natalensis

text: heart

text: Cryptomys hottentotus natalensis

text: female


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

characteristic: individual

text: not applicable

characteristic: isolate

text: Cryptomys hottentotus pretoriae

text: Cryptomys hottentotus pretoriae

text: heart

text: Cryptomys hottentotus pretoriae

text: female


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Cryptomys hottentotus pretoriae

text: Cryptomys hottentotus pretoriae

text: heart

characteristic: organism part

text: Cryptomys hottentotus pretoriae

text: male

characteristic: sex


text: QMUL

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: CHPA

text: not applicable

text: Cryptomys hottentotus pretoriae

text: Cryptomys hottentotus pretoriae

text: heart

text: Cryptomys hottentotus pretoriae

text: female

text: CHPA


characteristic: ENA first public

text: QMUL

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: adult

text: wild type genotype

text: not collected

text: CHPD

text: not applicable

text: Cryptomys hottentotus pretoriae

text: Cryptomys hottentotus pretoriae

text: heart

text: Cryptomys hottentotus pretoriae

text: female

text: CHPD


text: QMUL

text: public

text: ArrayExpress

text: not collected

characteristic: collection date

text: Damara mole-rat

characteristic: common name

text: adult

text: wild type genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Fukomys damarensis

text: Fukomys damarensis

text: heart

text: Fukomys damarensis

text: female


characteristic: ENA-CHECKLIST

text: QMUL

text: public

text: ArrayExpress

text: not collected

text: Damara mole-rat

characteristic: description

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Fukomys damarensis

characteristic: organism

text: Fukomys damarensis

text: heart

text: Fukomys damarensis

text: male


text: QMUL

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: not collected

text: Damara mole-rat

text: adult

text: wild type genotype

text: not collected

text: FDB

text: not applicable

text: Fukomys damarensis

text: Fukomys damarensis

text: heart

text: Fukomys damarensis

text: female

text: FDB

characteristic: title


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: Cape mole-rat

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: individual

text: not applicable

text: Georychus capensis

text: Georychus capensis

text: heart

text: Georychus capensis

text: male


text: QMUL

text: public

text: ArrayExpress

text: not collected

text: Cape mole-rat

text: adult

text: wild type genotype

text: not collected

text: not applicable

characteristic: isolate

text: Georychus capensis

text: Georychus capensis

text: heart

characteristic: organism part

text: Georychus capensis

text: female

characteristic: sex


characteristic: ENA first public

text: QMUL

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: naked mole-rat

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Heterocephalus glaber

text: Heterocephalus glaber

text: heart

text: Heterocephalus glaber

text: female


text: QMUL

text: public

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: naked mole-rat

characteristic: common name

text: adult

text: wild type genotype

text: not collected

text: not applicable

text: Heterocephalus glaber

text: Heterocephalus glaber

text: heart

text: Heterocephalus glaber

text: male


characteristic: ENA-CHECKLIST

text: WDRC KAUST

text: public

text: wastewater

characteristic: environment (biome)

text: municipal ww

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Metatranscriptome

characteristic: investigation type

text: metagenome

text: WWTPs monitor

characteristic: project name

text: metagenome

text: Illumina Miseq

characteristic: sequencing method

text: WWTPs

text: influent

characteristic: wastewater/sludge environmental package


characteristic: ENA first public

text: WDRC KAUST

text: public

characteristic: SRA accession

text: wastewater

text: municipal ww

text: water

text: Saudi Arabia

text: Metatranscriptome

text: metagenome

characteristic: organism

text: WWTPs monitor

text: metagenome

text: Illumina Miseq

text: WWTPs

characteristic: title


text: WDRC KAUST

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: collection date

text: wastewater

text: municipal ww

text: water

text: Saudi Arabia

text: metagenome

text: metagenome

text: WWTPs monitor

text: metagenome

text: Illumina Miseq

text: WWTPs

text: influent


characteristic: ENA-CHECKLIST

text: WDRC KAUST

text: public

text: wastewater

characteristic: environment (biome)

text: municipal ww

characteristic: environment (feature)

text: water

text: Saudi Arabia

text: metagenome

text: metagenome

text: WWTPs monitor

text: metagenome

text: Illumina Miseq

text: WWTPs


text: Durham University

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: Protocols: Human Subjects Informed consent for research studies, according to the protocols approved by Yorkshire and the Humber Research Ethics Committee (REC ref: 15/YH/0365), was obtained for all study participants. Information on the patient and control participants is provided in Table S1.  Derivation and characterisation of RP13-iPSCs We ascertained three related RP type 13 patients with a PRPF8 c.6926A>C (p.H2309P) heterozygous missense mutation characterised by night blindness in the first decade of life, and one patient with a de novo PRPF8 c.6926A>C heterozygous mutation displaying night blindness at the age of 8 years (Table S1) (Towns et al., 2010). Dermal skin fibroblasts were reprogrammed to iPSCs using a non-integrative RNA-based Sendai virus system (Figure S1A), as described in Buskin et al. 2018. Several clones from each RP13 participant were tested for expression of pluripotent markers (Figure S1B), clearance of transgenes (Figure S1C) and genome stability (Figure S1D). Apart from clone RP13-1A1, which displayed a decreased copy number in the Chr 12p region, all the other clones displayed the expected copy number in the loci that are most susceptible to changes in pluripotent stem cells. Based on these data, one iPSC clone from each participant was selected for further studies and referred to as RP13-1A, 1B, 1C, and 2 as shown in Table S1. All iPSCs were maintained in Matrigel-coated plates with mTeSR™ Plus media and passaged using Versene (EDTA 0.02%) in 1:3 -1: 6 ratio. All cultures were maintained at 37°C, in a humidified environment, with 5% CO2. Cells were cryopreserved with freezing media containing 90% foetal bovine serum (FBS), 10% dimethyl sulfoxide and 10 µM Y26732.  Sendai Virus Clearance assay Total RNA was extracted from 5 × 106 iPSCs using TRIzol® reagent following the manufacturer’s instructions. Reverse transcription was carried out using 1 µg of total RNA and the SuperScript cDNA Synthesis Kit following the manufacturer’s instructions. Polymerase chain reaction (PCR) was carried out using the cDNA from the reverse transcription reaction with GoTaq DNA polymerase. The PCR products were analysed using 2% agarose gel electrophoresis. All primer details are shown in Table S13.   Detection of pluripotency markers by flow cytometry  iPSCs were dissociated by incubation with Accutase for 5 minutes at 37℃. A total of 1x106 single cells were resuspended in PBS supplemented with 5% fetal calf serum (FCS) and stained with anti-TRA-1-60 antibody (directly conjugated to FITC, 1:50) and anti-NANOG antibody (directly conjugated to AlexFluor647 conjugate, 1:50) for two hours at 2-8°C followed by PBS washing and subjected to flow cytometry analysis using FACSCanto flow cytometer (BD Biosciences). At least 10,000 cells were acquired, and the data was analysed using the FACSDiva software.  Pluripotest analysis  100 ng total RNA extracted from each RP13 and isogenic control iPSCs was used to prepare the GeneChip® for the PluriTest™ analysis to generate a Pluripotency and Novelty Score. The Pluripotency Score is based on many samples (pluripotent, somatic, and tissues) in the stem cell model matrix which consists of an extensive reference set of >450 cell/tissue types, including 223 hESC lines, 41 iPSCs, somatic cells, and tissues. Samples with positive Pluripotency Scores are more similar to pluripotent samples in the model matrix than to all other classes of samples. The Novelty Score is based on well-characterised iPSCs in the stem cell model matrix.  Genome stability assays Genome stability was assessed using the hPSC Genetic Analysis kit or the Karyostat assay (Thermofisher). hPSC Genetic Analysis Kit: Genomic DNA from the patient iPSCs was harvested using genomic DNA extraction kit. Genomic DNA was mixed with 2x qPCR master mix and ROX reference dye for qPCR analysis. Nine pairs of primers were applied for the examination of Chromosome regions 1q, 4p, 8q, 10p, 12p, 12q, 18q, 20q and Xp. qPCR ∆∆Ct values were normalised to normal control iPSCs. A copy number < 1.8 or > 2.2 with a p-value <0.05 may indicate the presence of a cytogenetic abnormality. Karyostat Assay: To verify the genome stability of derived iPSCs, 250ng total genomic DNA extracted from each cell line was used in GeneChip® for KaryoStat™ assays for assessment of potential copy number variants or single nucleotide polymorphisms across the genome. The KaryoStat™ assay allows digital visualisation of chromosome aberrations with a resolution similar to G-band karyotyping. The size of structural aberration that can be detected is >2Mb for chromosomal gains and >1Mb for chromosomal losses. The KaryoStat™ array is optimised for balanced whole-genome coverage with a low-resolution DNA copy number analysis. The assay covers all 36,000 RefSeq genes, including 14,000 OMIM® targets, allowing the detection of aneuploidies, submicroscopic aberrations, and mosaic events.  Correction of PRPF8 mutation in RP13-iPSCs using CRISPR/Cas9 To fully understand the impact of PRPF8 mutation in RPE and retinal cells, CRISPR/Cas9 genome editing was used to correct the PRPF8 c.6926A>C genetic mutation in all patient iPSCs using protocols described in Buskin et al. 2018. For in situ gene correction, a guide RNA was designed to include the PRPF8 c. 6926A>C mutation in the 3’ region as well as an asymmetric ssODN template with wild-type PRPF8 sequence with the PAM sequence silenced to prevent repeated cleavage by Cas9 (Figure S2A). 100 iPSC clones from each patient were selected and tested by restriction site analysis using ApaL1, which cleaves the wild-type sequence “GTGCAC”. Approximately 20% of the clones showed complete digestion by ApaL1 (Figure S2B): these were further analysed by Sanger sequencing, which demonstrated the correction of the heterozygous mutation “A/C” to homozygous wild type “A” (Figure S2C). To exclude possible off-targeting effects, we tested five candidate genomic regions containing sequences partially matched to the gRNA (Table S10). All the candidate regions showed DNA sequences that match the wild type without insertion or deletion, indicating that no off-targeting occurred during the CRISPR/Cas9 genome editing procedure (Figure S2D). KaryoStat™ analysis, which assesses copy number variants and single nucleotide polymorphisms across the genome (Figure S2E) revealed the lack of genomic instabilities in the corrected clones. The CRISPR/Cas9 RP13-iPSC clones displayed high pluripotency scores in the PluriTest™ analysis (Figure S2F), confirming their pluripotent phenotype. From herein, unedited iPSCs that harbour the pathogenic c.6926A>C mutation in PRPF8 are collectively referred to as “RP13”. Similarly, the edited isogenic controls (c.6926C>A) are referred to as “RP13-Cas9”.  Differentiation of iPSCs to RPE Cells Differentiation was performed as previously described (Regents et al., 2019). In brief, RP13 and RP13-Cas9 iPSCs were grown on 6 well plates coated with growth factor-reduced Matrigel™, as recommended by the manufacturer’s. Cells were incubated at 37⁰C, 5% CO2 and fed every second day with 2 ml mTeSR™ Plus per well. Once iPSCs achieved 80-95% confluency, mTeSR™ Plus media was replaced with 3 ml of differentiation medium (DMEM/F-12, 50 μM β-mercaptoethanol, 1X MEM NEAA, 1X penicillin streptomycin, 20% knockout serum replacement and 10 mM nicotinamide). Differentiation media was partially changed every second day. On days 8 and day 14 media composition was adjusted, by omitting nicotinamide and adding 100 ng/ml Activin A or 3 µM CHIR99021, respectively (Figure 1A). RPE patches formed during this time and were manually excised using a scalpel and transferred to a Falcon tube containing differentiation media. Next, media was aspirated, and patches were washed quickly with PBS. Then patches were dissociated by incubation at 37°C with TryplE Select (10X) for approximately 20 minutes followed by passage through a 40 µm cell strainer. TryplE Select was neutralised with RPE media and cells were centrifuged for 5 minutes at 300 x g. Media was aspirated and replaced with fresh RPE maintenance media (DMEM/F-12, 50 µM β-mercaptoethanol, 1X MEM NEAA, 1X penicillin streptomycin, and 4% knockout serum replacement). iPSC-RPE were counted using a haemocytometer and plated at density of 1.5x105/cm2 on 6 well plates coated with growth factor-reduced Matrigel™ in 3 ml RPE maintenance media. Media was partially replaced every 2-3 days until cells were pigmented and had a typical “cobblestone” epithelial cell morphology. Cells were then dissociated using TryplE Select (10X) as described, and plated onto 24-well and 12-well PET 0.4 µm pore Transwell ThinCerts™.  Immunofluorescent Staining of iPSC-RPE cells iPSC-RPE cells grown on 24-well ThinCerts™ were washed with PBS and incubated with 4% paraformaldehyde (PFA) for 20 minutes at room temperature. PFA was then removed, cells were rinsed twice with PBS and stored in PBS at 4°C until required. The transwell culture surface was isolated and placed on Superfrost+ microscope slide. Pigmentation of RPE cells was removed using Melanin Bleach Kit, as recommended by the manufacturer. RPE cells were blocked in PBS supplemented with 10% normal donkey serum and 0.3% Triton-X100, for 1 hour at room temperature. For ezrin immunostaining, RPE cells were not bleached, and Triton X-100 was substituted for a 5-minute incubation at -20°C with methanol, prior to blocking. The RPE cells were incubated with primary antibodies overnight at 4°C. Following three washing with PBS, RPE cells were incubated with secondary antibodies diluted in antibody dilution (PBS and 1% normal donkey serum) with Hoechst for 1 hour at room temperature. Then, iPSC-RPE cells were washed 3X for 5 minutes with PBS before mounting with Vectashield and sealed with a #1 coverslip. RPE cells were imaged using an AxioImager upright microscope with Apotome structured illumination fluorescence using 20x, 40x and 63x oil objectives (Zeiss, Germany). Three to five images per patient were processed using ZEN 2.5 Lite software (Zeiss). For cilia studies, RPE cells were imaged using an 100x objective on an A1R confocal microscope (Nikon). Images were analysed using Fiji (ImageLab) to assess co-localisation of ciliary proteins, and Huygens software (Scientific Volume Imaging) to determine cilia length. Data were analyzed and processed in Prism 7 (GraphPad).  Measurement of trans-epithelial resistance (TER) Trans-epithelial resistance (TER) was measured in Transwells (containing RPE cells by inserting the tip of the short electrode in the inner side of the Transwell insert, and the tip of the longer electrode in the outer side of the Transwell insert. Also, the resistance of a blank TW containing PBS was measured. Three measurements were obtained from each Transwell insert. After that, the readings from the blank Transwell was subtracted from the readings obtained from Transwells containing RPE cells. Based on the formula Unit area resistance = Resistance (Ω) x Effective Membrane Area (cm2), the results were multiplied by 0.3, which is the membrane area of a Transwell, and final values were given in ohms (Ω). TER measurements were performed one day after feeding the RPE cells to avoid variability in the TER readings.  Phagocytosis assay Bovine rod photoreceptor outer segments (POSs) were centrifuged at 2600 × g for 4 minutes, and the pellet was resuspended with 0.4 mg/ml FITC for 1 hour at room temperature followed by agitation in the dark. Following centrifugation at 2600 × g for 4 minutes and washing of the POSs three times with PBS, POSs were resuspended in AdRPMI 1640 media supplemented with B-27 Supplement and FBS. The staining of POSs was confirmed under a Bioscience Axiovert microscope. RPE cells were treated with unlabelled and FITC-labelled POSs (20 POSs per cell) and incubated for 4 hours at 37°C. For control, RPE cells were treated with FITC-labelled POSs and were incubated at 4°C for 4 hours. Both control and RP13-RPE cells were washed with PBS and were detached from the wells using 200μl of TryplE Select (10X) for 15 minutes. Then, control and RP13-RPE cells were resuspended in flow buffer (PBS with 2% FBS) and were transferred into Eppendorf tubes followed by centrifugation at 300 × g. To distinguish cells from debris and unbound POSs, RPE cells were incubated with 5 mM DRAQ5 for 5 minutes. To quench fluorescence from unbound POSs, cells were incubated with 0.2% Trypan Blue solution for 10 minutes. RPE cells were washed 3 times with PBS, and cell pellets were resuspended in flow buffer. Samples were run on a LSRII flow cytometer, and 10,000 events were collected per sample. Results were analysed using FacsDiva software.   RPE cytokine secretion studies Medium from basal and apical chambers of transwell inserts were collected from RPE cells of healthy controls and patients. The levels of PEDF and VEGF secretion were measured by using human PEDF-ELISA Kit (Cusabio, CSB-E08818h) and human VEGF-ELISA Kit (Life Technologies) according to the manufacturer’s instructions.  Retinal organoids differentiation from iPSCs 7000 iPSCs were seeded into each well of Lipidure-coated 96-well U-bottomed plate and cultured for 48 hours to form Embryonic Bodies before start of differentiation. From day 0 to day 18, the differentiation medium was added into the culture containing 41% IMDM, 41% HAM’s F12, 15% KOSR, 1% GlutaMAX, 1% Chemically defined, lipid concentrate, 1% Pen/Strep, 450 μM (20 μl of stock) 1-Thioglycerol. 1.5nM BMP4 was added from day 6 to day 9 (Figure S4A). From day 18, the culture medium was changed to 10% FBS in DMEM/F12 supplemented with 1x N2, 0.1mM taurine and 0.5 μM retinoic acid until day 150.   Immunofluorescent Staining of iPSC-Retinal Organoids  Ten 10 µm thickness sections of retinal organoids were collected on glass cover slips and were separated using an ImmEdge pen. Sections were air-dried for 20 minutes at room temperature and washed with PBS to remove OCT 91 from the tissue. Retinal organoids sections were incubated with a blocking solution (5% normal goat or donkey serum, 0.3% Triton-X in PBS) for 1 hour at room temperature, followed by overnight incubation with primary polyclonal non-conjugated antibodies shown in the Key Resources Table at 4°C. Primary antibodies were diluted in antibody diluent solution containing PBS, 1% bovine serum albumin (BSA) and 0.3% Triton-X. Following overnight incubation, retinal sections were washed three times with PBS for 15 minutes each and incubated with secondary antibodies conjugated to fluorophores and diluted in antibody diluent for 1 hour at room temperature. Retinal organoids sections were then washed three times with PBS for 10 minutes each to remove unspecific binding. To detect nuclear staining, sections were covered by Hoechst nuclear stain diluted in Vectashield at 1:2000, followed by mounting of the slides by a coverslip.  Kidney organoid differentiation from iPSCs Kidney cell and organoid culture was based on established protocols (Takasato et al., 2015). In summary, RP13 and RP13-Cas9 iPSCs were cultured in mTeSR™ Plus as described above. To start differentiation into kidney cells, iPSCs were dissociated into single cells with TryplE. 400,000 cells were plated in Matrigel-coated 6-well plate with 2 ml mTeSR™ Plus containing 10 μM ROCK inhibitor (Y-27632) and incubated overnight (day -1). The next day, cells were at 50% confluency and media was changed to APEL2 containing 5% protein-free hybridoma medium (PFHM-II) (complete medium; henceforth called APEL2+) and 8 μM CHIR99021 (day 0). The same media change was done on day 2. On day 4 of differentiation, media was changed to APEL2+ containing 200 ng/ml FGF9 and 1 μg/ml heparin. Media was changed every other day. On day 7 of differentiation, kidney cells were trypsinised, resuspended into a single cell suspension and counted. 500,000 cells were transferred to an Eppendorf tube and spun down at 800 x g for 3 minutes at room temperature three times, with gentle tube agitation after each spin. 3D kidney organoid cultures were grown on an air-liquid interphase, on cell culture inserts called Thincerts (Greiner Bio-One Ltd). Kidney cell pellets were transferred into the inner part of the Thincert, and kidney organoids were allowed to mature. APEL2+ containing 5 μM CHIR99021 was added to the outer part of the Thincert and incubated for 1 hour at 37°C, following media change to APEL2+ containing 1x antibiotic/antimycotic (complete media; henceforth called APEL2++), 200 ng/ml FGF9 and 1 μg/ml heparin. Media containing growth factors was changed every other day throughout the differentiation. Growth factors were withdrawn on day 12 and culture with APEL2++ media was carried on until day 25.  Cyst induction A 24-well plate was coated with Lipidure by placing 500 μl of 0.5% w/v Lipidure solution in each well and allowing complete evaporation at room temperature in sterile conditions. On day 22, kidney organoids were moved from Thincerts into a non-adherent plate with APEL2++ media containing 30 μM forskolin, 12.5 μM blebbistatin or DMSO. Organoids were grown in suspension with drugs for 72 hours.  Kidney organoids processing On day 25 organoids were washed with PBS and snap-frozen in liquid nitrogen for biochemical and proteomic assays. Organoids for RNA sequencing were suspended in 1 ml Trizol and snap-frozen. Organoids for immunofluorescent staining were fixed with 4% PFA for a minimum of 4 hours, followed by three PBS washes. They were permeabilized and blocked using 2% BSA in PBS containing 0.3% Triton X-100 overnight at 4°C. After three PBS washes, organoids were incubated in primary antibodies diluted in 1% BSA overnight at 4°C. Following three PBS washes, organoids were incubated in secondary antibodies diluted in 1% BSA overnight at 4°C. On the final day, organoids were washed three times with PBS and imaged with a confocal A1R microscope (Nikon) at x4 magnification. Organoids for OCT embedding were fixed with 4% PFA, washed with PBS and soaked in 30% (w/v) sterile sucrose overnight at 4°C on a roller. Following a PBS wash, organoids were placed in moulds, submerged in OCT and frozen. Frozen OCT blocks were cryosectioned at 10 μm thickness on a Leica CM1950 cryostat. Sectioned organoids were stored at -80°C until use. Further processing was as described below. Images were processed in Fiji (ImageJ). Image processing included the use of the following plugins: “Colocalisation Threshold”, “CiliaQ” and “Mitochondria Analyser”.  Kidney cell and organoid culture was based on established protocols (Takasato et al., 2015). In summary, RP13 and RP13-Cas9 iPSCs were cultured in mTeSR™ Plus as described above. To start differentiation into kidney cells, iPSCs were dissociated into single cells with TryplE. 400,000 cells were plated in Matrigel-coated 6-well plate with 2 ml mTeSR™ Plus containing 10 μM ROCK inhibitor (Y-27632) and incubated overnight (day -1). The next day, cells were at 50% confluency and media was changed to APEL2 containing 5% protein-free hybridoma medium (PFHM-II) (complete medium; henceforth called APEL2+) and 8 μM CHIR99021 (day 0). The same media change was done on day 2. On day 4 of differentiation, media was changed to APEL2+ containing 200 ng/ml FGF9 and 1 μg/ml heparin. Media was changed every other day. On day 7 of differentiation, kidney cells were trypsinised, resuspended into a single cell suspension and counted. 500,000 cells were transferred to an Eppendorf tube and spun down at 800 x g for 3 minutes at room temperature three times, with gentle tube agitation after each spin. 3D kidney organoid cultures were grown on an air-liquid interphase, on cell culture inserts called Thincerts (Greiner Bio-One Ltd). Kidney cell pellets were transferred into the inner part of the Thincert, and kidney organoids were allowed to mature. APEL2+ containing 5 μM CHIR99021 was added to the outer part of the Thincert and incubated for 1 hour at 37°C, following media change to APEL2+ containing 1x antibiotic/antimycotic (complete media; henceforth called APEL2++), 200 ng/ml FGF9 and 1 μg/ml heparin. Media containing growth factors was changed every other day throughout the differentiation. Growth factors were withdrawn on day 12 and culture with APEL2++ media was carried on until day 25. Correction of PRPF8 mutation in RP13-iPSCs using CRISPR/Cas9 To fully understand the impact of PRPF8 mutation in RPE and retinal cells, CRISPR/Cas9 genome editing was used to correct the PRPF8 c.6926A>C genetic mutation in all patient iPSCs using protocols described in Buskin et al. 2018. For in situ gene correction, a guide RNA was designed to include the PRPF8 c. 6926A>C mutation in the 3’ region as well as an asymmetric ssODN template with wild-type PRPF8 sequence with the PAM sequence silenced to prevent repeated cleavage by Cas9 (Figure S2A). 100 iPSC clones from each patient were selected and tested by restriction site analysis using ApaL1, which cleaves the wild-type sequence “GTGCAC”. Approximately 20% of the clones showed complete digestion by ApaL1 (Figure S2B): these were further analysed by Sanger sequencing, which demonstrated the correction of the heterozygous mutation “A/C” to homozygous wild type “A” (Figure S2C). To exclude possible off-targeting effects, we tested five candidate genomic regions containing sequences partially matched to the gRNA (Table S10). All the candidate regions showed DNA sequences that match the wild type without insertion or deletion, indicating that no off-targeting occurred during the CRISPR/Cas9 genome editing procedure (Figure S2D). KaryoStat™ analysis, which assesses copy number variants and single nucleotide polymorphisms across the genome (Figure S2E) revealed the lack of genomic instabilities in the corrected clones. The CRISPR/Cas9 RP13-iPSC clones displayed high pluripotency scores in the PluriTest™ analysis (Figure S2F), confirming their pluripotent phenotype. From herein, unedited iPSCs that harbour the pathogenic c.6926A>C mutation in PRPF8 are collectively referred to as “RP13”. Similarly, the edited isogenic controls (c.6926C>A) are referred to as “RP13-Cas9”.  Trizol suspensions of iPSCs, RPEs, kidney and retinal organoids were homogenized using 26-gauge syringe needles followed by standard Trizol RNA extraction. Extracted RNA was further purified using DNAse TURBO, and RNA purity and concentration was evaluated on TapeStation (Agilent Technologies).  RNA libraries were prepared using TruSeq Stranded mRNA libraries

characteristic: description

text: Retinitis pigmentosa

characteristic: disease

text: corrected

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: organoid culture

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney organoid

characteristic: organism part

text: Homo sapiens