text: Cancer Research UK Cambridge Institute.

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: somite 35

text: posterior

text: Mus musculus

text: male


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Cambridge Institute.

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Cancer Research UK Cambridge Institute.

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Mouse embryos from the appropriate somite stages (8 to 35 somites) were dissected in RNAse-free conditions in cold PBS, on silicone plates. To dissect out the somites, embryos were treated with dispase II (1mg/mL in DMEM) for 30-45 seconds at 37°C. The three most posterior pairs of somites were then collected using tungsten needles, dissecting out every somite separately. We labelled each somite pair as somite I, II or III, from the most posterior to the most anterior, respectively. Each individual somite was placed in 10µL of lysis buffer (Takara) containing RNase inhibitor. One somite from each pair was flash frozen in liquid nitrogen and stored at -80°C for later processing for RNA-seq. The matching somites were directly processed to generate ATAC-seq libraries. Individual somites were transposed with 1µL of transposome (Nextera DNA Sample Preparation kit FC-121-1030) at 37°C for 30 minutes. Samples were then purified with the Zymo Clean & Concentrator kit and eluted in 21µL of elution buffer. Transposed DNA was quantified by qPCR using 5 μl of PCR products. The number of additional cycles was determined by plotting linear Rn versus cycle and corresponded to one third of the maximum fluorescence intensity. Transposed DNA was then amplified with 13 cycles of PCR. The final products were double size-selected with AMPure beads (0.55X - 1.5X) to obtain fragments between 100bp and 700bp. Libraries were quantified and the sizes were assessed with a TapeStation machine.

characteristic: description

text: embryo stage

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: somite 35

characteristic: organism part

text: medial

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


text: Cancer Research UK Cambridge Institute.

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: somite 35

text: anterior

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Cambridge Institute.

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: house mouse

text: embryo stage

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: somite 35

text: posterior

text: Mus musculus

text: female


text: Cancer Research UK Cambridge Institute.

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo stage

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: somite 35

characteristic: organism part

text: medial

text: Mus musculus

text: female


text: Cancer Research UK Cambridge Institute.

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

text: embryo stage

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: somite 35

text: anterior

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Cancer Research UK Cambridge Institute.

text: public

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryo stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: somite 27

text: posterior

text: Mus musculus

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Cancer Research UK Cambridge Institute.

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: embryo stage

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: somite 27

text: medial

text: Mus musculus

text: female


text: Cancer Research UK Cambridge Institute.

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: embryo stage

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: somite 27

characteristic: organism part

text: anterior

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: BIOMERIEUX

text: public

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:498-122056

characteristic: collection date

text: Serbia

characteristic: geographic location (country and/or sea)

text: wastewater

text: Enterobacter hormaechei

text: Enterobacter hormaechei

characteristic: title


characteristic: ENA-LAST-UPDATE

text: BIOMERIEUX

text: public

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:498-122057

text: Serbia

text: wastewater

text: Enterobacter asburiae

text: Enterobacter asburiae


characteristic: External Id

text: BIOMERIEUX

text: public

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:498-122059

text: Serbia

text: wastewater

text: Enterobacter kobei

text: Enterobacter kobei


text: BIOMERIEUX

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:499-122060

text: Serbia

text: wastewater

text: Enterobacter roggenkampii

text: Enterobacter roggenkampii


text: BIOMERIEUX

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:499-122062

text: Serbia

text: wastewater

text: Enterobacter roggenkampii

text: Enterobacter roggenkampii


text: BIOMERIEUX

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:499-122063

text: Serbia

text: wastewater

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: BIOMERIEUX

text: public

text: ena-SAMPLE-TAB-09-01-2023-16:24:03:499-122064

characteristic: Submitter Id

text: Serbia

text: wastewater

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: NIPH

characteristic: INSDC center name

text: public

text: ELIXIR-Norway

characteristic: broker name

text: Norway

text: not provided

characteristic: host health state

text: Homo Sapiens

characteristic: host scientific name

characteristic: isolate

text: Blood

text: Neisseria meningitidis

text: Neisseria meningitidis


text: University of Helsinki

characteristic: INSDC first public

text: public

tag: Namespace:University of Helsinki

text: Finnish institute for health and welfare

text: Carbapenemase-producing C. freundii clinical sample

characteristic: description

text: Citrobacter freundii

characteristic: organism

text: Citrobacter freundii


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University of Helsinki

text: public

text: Carbapenemase-producing C. freundi hospital environment sample

text: Citrobacter freundii

text: Citrobacter freundii


text: University of Helsinki

text: public

text: University of Helsinki

text: Citrobacter freundii

text: Citrobacter freundii

characteristic: title


characteristic: ENA-LAST-UPDATE

text: University of Helsinki

text: public

text: University of Helsinki

text: Carbapenemase-producing C. freundi wastewater sample

text: Citrobacter freundii

text: Citrobacter freundii


characteristic: External Id

text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

characteristic: geographic location (country and/or sea)

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 1


text: ISCIII

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 2


text: ISCIII

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 3


text: ISCIII

characteristic: INSDC center name

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 4


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 5


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 6


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 7


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 8


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 9


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 10


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 11


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 12


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 13


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 14


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 15


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 16


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 17


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 18


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 19


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 20


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 21


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 22


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 23


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 24


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 25


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 26


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 27


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 28


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 29


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 30


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 31


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 32


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 33


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 34


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 35


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 36


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 37


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 38


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 39


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 40


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 41


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 42


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 43


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 44


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 45


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 46


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 47


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 48


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 49


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 50


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 51


text: ISCIII

text: public

text: ISCIII

text: not provided

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 52


text: ISCIII

text: public

text: ISCIII

text: K. pneumoniae clinical sample

text: Spain

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 53


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 54


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 55


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 56


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 57


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 58


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 59


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 60


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 61


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 62


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 63


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 64


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 65


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 66


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 67


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 68


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 69


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 70


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 71


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 72


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 73


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 74


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 75


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 76


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 77


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 78


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 79


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 80


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 81


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 82


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 83


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 84


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 85


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 86


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 87


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 88


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 89


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 90


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 91


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 92


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 93


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 94


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 95


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 96


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 97


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 98


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 99


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 100


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 101


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 102


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 104


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 105


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 106


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 107


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 108


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 109


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 110


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 111


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 112


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 113


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 114


text: ISCIII

text: public

text: RIVM

text: not provided

text: K. pneumoniae clinical sample

text: Netherlands

text: Homo Sapiens

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: K. pneumoniae sample 115


LMG 1352

text: Ghent University

text: public

text: LMG 1352

tag: Namespace:Ghent University

text: Bombella apis LMG 1352

text: Spain

text: Madrid area

characteristic: geographic location (region and locality)

text: Rodriguez-Navarro A4-1

text: Beehive

text: Bombella apis

text: Bombella apis

text: LMG 1352

characteristic: strain

text: Bombella apis LMG 1352


LMG 30241

text: Ghent University

text: public

text: LMG 30241

text: Bombella apis LMG 30241

text: Belgium

text: Ghent, Coupure

characteristic: isolate

text: Bumblebee, B. lapidarius

text: Bombella apis

text: Bombella apis

text: LMG 30241

text: Bombella apis LMG 30241


LMG 32855

text: Ghent University

characteristic: INSDC first public

text: public

text: LMG 32855

text: Hafnia alvei LMG 32855

text: Belgium

text: Ghent, Bourgoyen

text: Bumblebee, B. hypnorum

text: Hafnia alvei

text: Hafnia alvei

text: LMG 32855

text: Hafnia alvei LMG 32855


LMG 32856

text: Ghent University

text: public

text: LMG 32856

text: Hafnia alve LMG 32856

characteristic: description

text: Belgium

text: Ghent, Bourgoyen

text: Bumblebee, B. lapidarius

text: Hafnia alvei

text: Hafnia alvei

text: LMG 32856

text: Hafnia alve LMG 32856


LMG 32857

text: Ghent University

text: public

text: LMG 32857

text: Hafnia alvei LMG 32857

text: Belgium

text: Wetteren

text: Bumblebee, B. lucorum

text: Hafnia alvei

characteristic: organism

text: Hafnia alvei

text: LMG 32857

text: Hafnia alvei LMG 32857


LMG 32858

characteristic: ENA-CHECKLIST

text: Ghent University

text: public

text: LMG 32858

text: Hafnia alvei LMG 32858

text: Belgium

text: Ghent, Bourgoyen

text: Bumblebee, B. pascuorum

text: Hafnia alvei

text: Hafnia alvei

text: LMG 32858

text: Hafnia alvei LMG 32858


LMG 32859

characteristic: ENA-FIRST-PUBLIC

text: Ghent University

text: public

text: LMG 32859

text: Hafnia alvei LMG 32859

text: Belgium

text: Ghent, Bourgoyen

text: Bumblebee, B. terrestris

text: Hafnia alvei

text: Hafnia alvei

text: LMG 32859

text: Hafnia alvei LMG 32859


LMG 32860

text: Ghent University

text: public

text: LMG 32860

text: Hafnia alvei LMG 32860

text: Belgium

text: Wetteren

text: Bumblebee, B. terrestris

text: Hafnia alvei

text: Hafnia alvei

text: LMG 32860

text: Hafnia alvei LMG 32860

characteristic: title


LMG 32861

characteristic: ENA-LAST-UPDATE

text: Ghent University

text: public

text: LMG 32861

text: Lactococcus lactis LMG 32861

text: Belgium

text: Wetteren

text: Bumblebee, B. lucorum

text: Lactococcus lactis

text: Lactococcus lactis

text: LMG 32861

text: Lactococcus lactis LMG 32861


LMG 32862

characteristic: External Id

text: Ghent University

text: public

text: LMG 32862

text: Lactococcus lactis LMG 32862

text: Belgium

text: Wetteren

text: Bumblebee, B. lucorum

text: Lactococcus lactis

text: Lactococcus lactis

text: LMG 32862

text: Lactococcus lactis LMG 32862


LMG 32863

text: Ghent University

text: public

text: LMG 32863

text: Lactococcus lactis LMG 32863

text: Belgium

characteristic: geographic location (country and/or sea)

text: Gentbrugge

text: Bumblebee, B. terrestris

text: Lactococcus lactis

text: Lactococcus lactis

text: LMG 32863

text: Lactococcus lactis LMG 32863


LMG 32864

text: Ghent University

characteristic: INSDC last update

text: public

text: LMG 32864

text: Lactococcus lactis LMG 32864

text: Belgium

text: Ghent, Ledeganck botanical garden

text: Bumblebee, B. terrestris

text: Lactococcus lactis

text: Lactococcus lactis

text: LMG 32864

text: Lactococcus lactis LMG 32864


LMG 32865

text: Ghent University

text: public

characteristic: INSDC status

text: LMG 32865

text: Secundilactobacillus kimchicus LMG 32865

text: Belgium

text: Ghent, Bourgoyen

text: Bumblebee, B. terrestris

text: Secundilactobacillus kimchicus

text: Secundilactobacillus kimchicus

text: LMG 32865


LMG 32866

text: Ghent University

text: public

characteristic: SRA accession

text: LMG 32866

text: Secundilactobacillus kimchicus LMG 32866

text: Belgium

text: Gentbrugge

text: Bumblebee, B. terrestris

text: Secundilactobacillus kimchicus

text: Secundilactobacillus kimchicus

text: LMG 32866


LMG 30243

text: Ghent University

text: public

text: LMG 30243

characteristic: Submitter Id

text: Secundilactobacillus kimchicus LMG 30243

text: Belgium

text: Ghent, Ledeganck botanical garden

text: Bumblebee, B. terrestris

text: Secundilactobacillus kimchicus

text: Secundilactobacillus kimchicus

text: LMG 30243


LMG 30244

text: Ghent University

characteristic: INSDC center name

text: public

text: LMG 30244

text: Secundilactobacillus kimchicus LMG 30244

text: Belgium

text: Ghent, Ledeganck botanical garden

text: Bumblebee, B. terrestris

text: Secundilactobacillus kimchicus

text: Secundilactobacillus kimchicus

text: LMG 30244


text: STATENS SERUM INSTITUT

text: public

tag: Namespace:STATENS SERUM INSTITUT

text: Escherichia coli

text: Escherichia coli


characteristic: ENA first public

text: public

tag: Namespace:San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: leukocyte

text: house mouse

characteristic: common name

text: Protocols: Lungs were harvested at day 9 and digested to obtain single cell suspensions to be processed for scRNA analysis. CD45+ cells were isolated using ARIA Cell Sorter (BD). Single cell suspensions were processed for single cell analysis using Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10X Genomics) following manufacturer’s instructions. 8-weeks females C57/BL6 mice (4 mice per group) were injected with 5x10^4 KPneo cells intravenously. Lungs were harvested at day 9 post-inoculation. Mice were administered 30 ug of recombinant Flt3L on day -2, 2, 4 , 6. On day 5, mice received a single dose of aCD40 (200ug intraperitoneally). Control mice received intraperitoneal injections of PBS on day -2,2,4,6 and isotype rat aIgG on day 6. Nucleic acids (polyA RNA) were extracted during single cell encapsulation and immediately barcoded, according to Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10X Genomics) protocol. Libraries were constructed using Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10X Genomics) protocol and following manufacturer’s instructions.

text: adult

characteristic: developmental stage

text: KrasG12D/WT; Tp53

characteristic: genotype

text: CD45 positive

characteristic: immunophenotype

text: pool of 4 mice

characteristic: individual

text: not applicable

text: Mus musculus

text: Mus musculus

text: lung

characteristic: organism part

text: neoplasm

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: External Id

text: San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy

text: public

text: ArrayExpress

text: leukocyte

text: house mouse

characteristic: description

text: adult

text: KrasG12D/WT; Tp53

text: CD45 positive

text: pool of 4 mice

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: lung

text: neoplasm

text: Mus musculus

text: female

characteristic: strain

characteristic: title


E-MTAB-12503:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UZH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12503:Sample 3

characteristic: Submitter Id

unit: hour

characteristic: age

text: ArrayExpress

text: zebrafish

text: Protocols: Zebrafish embryos were collected at indicated developmental stages (tailbud stage and 24 hpf). Total RNA was isolated from genotype-defined, pooled embryos by Trizol LS extraction as per manufacturer’s guidelines (Invitrogen), with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit (Illumina).

text: pharyngula prim-5

text: Danio rerio

text: Danio rerio

text: embryo

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 3


E-MTAB-12503:Sample 4

text: UZH

text: public

text: E-MTAB-12503:Sample 4

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: pharyngula prim-5

characteristic: developmental stage

characteristic: genotype

characteristic: individual

text: Danio rerio

text: Danio rerio

text: embryo

characteristic: organism part

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 4


E-MTAB-12503:Sample 7

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UZH

text: public

text: E-MTAB-12503:Sample 7

text: ArrayExpress

text: zebrafish

characteristic: description

text: bud

text: Danio rerio

characteristic: organism

text: Danio rerio

text: embryo

text: Danio rerio

text: mixed AB and Tubingen

characteristic: strain

text: Sample 7


E-MTAB-12503:Sample 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UZH

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12503:Sample 1

text: ArrayExpress

text: zebrafish

text: pharyngula prim-5

text: wild type genotype

text: Danio rerio

text: Danio rerio

text: embryo

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 1

characteristic: title


E-MTAB-12503:Sample 2

text: UZH

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12503:Sample 2

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: zebrafish

text: pharyngula prim-5

text: wild type genotype

text: Danio rerio

text: Danio rerio

text: embryo

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 2


E-MTAB-12503:Sample 5

text: UZH

text: public

text: E-MTAB-12503:Sample 5

text: ArrayExpress

characteristic: broker name

text: zebrafish

characteristic: common name

text: bud

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Danio rerio

text: Danio rerio

text: embryo

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 5


E-MTAB-12503:Sample 6

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UZH

text: public

text: E-MTAB-12503:Sample 6

text: ArrayExpress

text: zebrafish

characteristic: description

text: bud

text: wild type genotype

text: Danio rerio

characteristic: organism

text: Danio rerio

text: embryo

characteristic: organism part

text: Danio rerio

text: mixed AB and Tubingen

text: Sample 6


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MPIPZ

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: fission yeast

text: Protocols: S. pombe cells were inoculated in liquid YES medium overnight at 32°C, diluted to 2-5 x 10exp6 cells/ml the next morning and grown for 6 hours. Next, cells were resuspended in liquid EMM at 1 x 10exp8 cells/ml and 1 ml was treated or not with 20 microliters of EMS (ie 2% final) for 3h in 10 ml tubes at 32°C. Next, cells were washed three times with 5 ml of EMM, resuspended in 1 ml of EMM, plated on YES plates and incubated at 32°C until colonies formed. S. pombe spores were grown to saturation in 1.6 ml of YES medium at 32°C in 96 well plates (2 ml deep well plates). Cells were harvested by centrifugation, washed once with TE and lyzed during two hours at 37°C using 30 units of zymolyase in Y1 Qiagen buffer. Samples were centrifuged at 2,700g for five minutes and supernatants treated with 0.5 mg/ml of RNaseA for 10 minutes at room temperature. DNA was next purified from these lysates using the E-Z 96™ Tissue DNA Kit from Omega Bio-tek following the manufacturer’s instructions except for DNA binding to the columns that was done by gravity flow instead of centrifugation. TPase-based DNA library (>95 samples)

text: wild type genotype

text: YES medium

characteristic: growth condition

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: whole organism

text: Schizosaccharomyces pombe

characteristic: strain


text: MPIPZ

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: fission yeast

text: h- leu1-32 ura4-D18

text: YES medium

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: whole organism

text: Schizosaccharomyces pombe

characteristic: title


text: MPIPZ

text: public

text: ArrayExpress

characteristic: broker name

text: fission yeast

characteristic: common name

text: h+ leu1-32 ura4-D18

characteristic: genotype

text: YES medium

text: Schizosaccharomyces pombe

text: Schizosaccharomyces pombe

text: whole organism

text: Schizosaccharomyces pombe


characteristic: ENA-CHECKLIST

characteristic: External Id

text: UNIVERSITY HOHENHEIM

text: public

tag: Namespace:UNIVERSITY HOHENHEIM

text: Fresgh grass

characteristic: description

text: Germany

characteristic: geographic location (country and/or sea)

text: silage metagenome

text: Viral and bacterial diversity in grass silage

characteristic: project name

text: silage metagenome

text: Day 0


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY HOHENHEIM

characteristic: INSDC center name

text: public

text: Grass ensilaging day , 1L bottle

text: Germany

text: silage metagenome

characteristic: organism

text: silage metagenome

text: Day 2


text: UNIVERSITY HOHENHEIM

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Grass ensilaging day 2, 1L bottle

text: Germany

text: silage metagenome

text: silage metagenome

text: Day 2


text: UNIVERSITY HOHENHEIM

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Grass ensilaging day 4, 1L bottle

text: Germany

text: silage metagenome

text: silage metagenome

text: Day 4


text: UNIVERSITY HOHENHEIM

text: public

characteristic: Submitter Id

text: Grass ensilaging day 8, 1L bottle

text: Germany

text: silage metagenome

text: silage metagenome

text: Day 8

characteristic: title


text: UNIVERSITY HOHENHEIM

text: public

text: Grass ensilaging day 15, 1L bottle

text: Germany

text: silage metagenome

text: silage metagenome

text: Day 15


text: UNIVERSITY HOHENHEIM

text: public

text: Grass ensilaging day 40, 1L bottle

text: Germany

text: silage metagenome

text: silage metagenome

text: Day 40


text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

text: public

tag: Namespace:Tree of Life Programme

text: EVA VAN DER HEIJDEN

text: Sanger Institute

characteristic: collecting institution

characteristic: collection date

unit: m

characteristic: elevation

text: Colombia

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Putumayo | Mocoa | Campucana

characteristic: geographic location (region and locality)

text: Tropical rainforest

characteristic: habitat

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

characteristic: lifestage

text: Melinaea mothone

text: HEAD | ABDOMEN

characteristic: organism part

characteristic: sample derived from

text: Melinaea mothone

text: FEMALE

characteristic: sex

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: Colombia

characteristic: geographic location (country and/or sea)

text: Putumayo | Mocoa | Campucana

text: Tropical rainforest

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

text: Melinaea mothone

characteristic: organism

text: THORAX

characteristic: project name

text: Melinaea mothone

text: FEMALE

text: N


text: Sanger Institute

characteristic: GAL

text: Tree of Life Programme

text: public

characteristic: Submitter Id

text: EVA VAN DER HEIJDEN

text: Sanger Institute

characteristic: collecting institution

characteristic: collection date

characteristic: elevation

text: Colombia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Putumayo | Mocoa | Campucana

characteristic: geographic location (region and locality)

text: Tropical rainforest

characteristic: habitat

text: EVA VAN DER HEIJDEN

text: Sanger Institute

text: adult

characteristic: lifestage

text: Melinaea mothone

text: LEG

characteristic: organism part

text: Melinaea mothone

text: FEMALE

text: N

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: PHAS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:029-8

text: PHAS

characteristic: broker name

text: not provided

characteristic: description

text: Sweden

text: Homo sapiens

characteristic: host scientific name

text: Culture

text: Campylobacter coli

text: Campylobacter coli


text: PHAS

text: public

characteristic: SRA accession

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:029-9

characteristic: Submitter Id

text: PHAS

text: not provided

characteristic: collection date

text: Sweden

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Culture

text: Yersinia enterocolitica

characteristic: organism

text: Yersinia enterocolitica


text: PHAS

text: public

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:030-10

text: PHAS

text: not provided

text: Sweden

text: Homo sapiens

text: Culture

text: Salmonella enterica

text: Salmonella enterica

characteristic: title


characteristic: ENA-CHECKLIST

text: PHAS

text: public

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:030-11

text: PHAS

text: not provided

text: Sweden

text: Homo sapiens

text: Culture

text: Campylobacter jejuni

text: Campylobacter jejuni


characteristic: ENA-FIRST-PUBLIC

text: PHAS

text: public

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:030-12

text: PHAS

text: not provided

text: Sweden

text: Homo sapiens

text: Culture

text: Salmonella enterica

text: Salmonella enterica


characteristic: ENA-LAST-UPDATE

text: PHAS

text: public

text: ena-SAMPLE-TAB-16-01-2023-14:23:13:030-13

text: PHAS

text: not provided

text: Sweden

text: Homo sapiens

text: Culture

text: Yersinia enterocolitica

text: Yersinia enterocolitica


characteristic: External Id

text: University of Milan-Bicocca

text: public

tag: Namespace:University of Milan-Bicocca

text: water

characteristic: broad-scale environmental context

characteristic: depth

text: water

text: water

characteristic: environmental medium

text: Italy

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: water

characteristic: local environmental context

text: uncultured bacterium

text: AGER

characteristic: project name

text: uncultured bacterium


text: University of Milan-Bicocca

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: water

text: tankbiofilm

characteristic: description

text: water

text: Italy

text: water

text: uncultured bacterium

text: AGER

text: uncultured bacterium


characteristic: ENA-CHECKLIST

text: Universitat Pompeu Fabra

text: public

tag: Namespace:Universitat Pompeu Fabra

characteristic: Submitter Id

text: human

characteristic: common name

text: iPSC edited with Cas9

text: Homo sapiens

characteristic: organism

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Universitat Pompeu Fabra

text: public

text: human

text: iPSC edited with SHE

text: Homo sapiens

text: Homo sapiens


text: UNIVERSITY HOSPITAL JENA

text: public

tag: Namespace:UNIVERSITY HOSPITAL JENA

text: routine

text: Germany

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

text: bacteria

characteristic: isolate

text: Hospital

text: Staphylococcus aureus

text: Staphylococcus aureus


text: UNIVERSITY HOSPITAL JENA

characteristic: INSDC center name

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: UNIVERSITY HOSPITAL JENA

characteristic: INSDC first public

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Acinetobacter sp. ATCC 11171

text: Acinetobacter sp. ATCC 11171


text: UNIVERSITY HOSPITAL JENA

characteristic: INSDC last update

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Escherichia coli

text: Escherichia coli


text: UNIVERSITY HOSPITAL JENA

text: public

characteristic: INSDC status

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Enterococcus faecium

text: Enterococcus faecium


text: UNIVERSITY HOSPITAL JENA

text: public

characteristic: SRA accession

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Enterobacter cloacae

text: Enterobacter cloacae


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

characteristic: description

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


characteristic: ENA-CHECKLIST

text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Pseudomonas asiatica

text: Pseudomonas asiatica


text: UNIVERSITY HOSPITAL JENA

text: public

characteristic: Submitter Id

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Citrobacter freundii

text: Citrobacter freundii


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Klebsiella oxytoca

text: Klebsiella oxytoca


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Citrobacter braakii

text: Citrobacter braakii


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Citrobacter farmeri

text: Citrobacter farmeri


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Enterobacter hormaechei

text: Enterobacter hormaechei


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Acinetobacter pittii

text: Acinetobacter pittii


text: UNIVERSITY HOSPITAL JENA

text: public

text: routine

text: Germany

text: Homo sapiens

text: bacteria

text: Hospital

text: Pseudomonas putida

text: Pseudomonas putida


text: University of Warmia and Mazury

text: public

tag: Namespace:University of Warmia and Mazury

text: house mouse

characteristic: common name

text: Sample 1 of control mice kidney

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 2 of control mice kidney

text: Mus musculus

characteristic: organism

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 3 of control mice kidney

text: Mus musculus

text: Mus musculus

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 4 of control mice kidney

text: Mus musculus

text: Mus musculus


characteristic: ENA-LAST-UPDATE

text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 5 of control mice kidney

text: Mus musculus

text: Mus musculus


characteristic: External Id

text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 6 of control mice kidney

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 1 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 2 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 3 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 4 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 5 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: University of Warmia and Mazury

text: public

text: house mouse

text: Sample 6 kidney of mice treated with BPA

text: Mus musculus

text: Mus musculus


text: UNIVERSITY OF COPENHAGEN

text: public

tag: Namespace:UNIVERSITY OF COPENHAGEN

text: not provided

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6800374 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Ligilactobacillus aviarius

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken ileum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Ligilactobacillus aviarius

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus aviarius

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6800374_bin.2_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769785 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Lactobacillus sp.

characteristic: organism

text: uncultured Lactobacillus sp.

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__

text: multi-marker approach

text: Binned metagenome: ERR6769785_bin.5_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889851 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Agathobaculum sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Agathobaculum sp.

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__Agathobaculum;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6889851_bin.30_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889849 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Merdibacter sp.

characteristic: organism

text: uncultured Merdibacter sp.

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

text: multi-marker approach

text: Binned metagenome: ERR6889849_bin.49_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769707 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Limosilactobacillus vaginalis

characteristic: project name

characteristic: sample derived from

text: Limosilactobacillus vaginalis

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus vaginalis

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769707_bin.2_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Oscillospiraceae bacterium

characteristic: organism

text: uncultured Oscillospiraceae bacterium

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__;s__

text: multi-marker approach

text: Binned metagenome: ERR6889849_bin.40_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769738 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus gallinarum

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken ileum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Lactobacillus gallinarum

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus gallinarum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769738_bin.1_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769768 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus agilis

characteristic: organism

text: Ligilactobacillus agilis

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus agilis

text: multi-marker approach

text: Binned metagenome: ERR6769768_bin.8_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769666 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Escherichia coli

characteristic: project name

characteristic: sample derived from

text: Escherichia coli

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769666_bin.3_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769784 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Limosilactobacillus oris

characteristic: organism

text: Limosilactobacillus oris

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus oris

text: multi-marker approach

text: Binned metagenome: ERR6769784_bin.1_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769665 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus crispatus

characteristic: project name

characteristic: sample derived from

text: Lactobacillus crispatus

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus crispatus

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769665_bin.2_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769707 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Limosilactobacillus reuteri

characteristic: organism

text: Limosilactobacillus reuteri

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus reuteri

text: multi-marker approach

text: Binned metagenome: ERR6769707_bin.5_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889851 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Eisenbergiella sp.

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken ileum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: uncultured Eisenbergiella sp.

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__Eisenbergiella;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6889851_bin.51_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769646 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Lactobacillus crispatus

characteristic: organism

text: Lactobacillus crispatus

text: multi-marker approach

text: Binned metagenome: ERR6769646_bin.1_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769773 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Lactobacillus gallinarum

characteristic: project name

characteristic: sample derived from

text: Lactobacillus gallinarum

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__Lactobacillus gallinarum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769773_bin.1_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889849 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Lachnospiraceae bacterium

characteristic: organism

text: uncultured Lachnospiraceae bacterium

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__;s__

text: multi-marker approach

text: Binned metagenome: ERR6889849_bin.15_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769729 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Enterococcus hirae

characteristic: project name

characteristic: sample derived from

text: Enterococcus hirae

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Enterococcaceae;g__Enterococcus;s__Enterococcus hirae

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769729_bin.2_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769698 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli

text: multi-marker approach

text: Binned metagenome: ERR6769698_bin.1_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769708 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Ligilactobacillus aviarius

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken ileum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

characteristic: project name

characteristic: sample derived from

text: Ligilactobacillus aviarius

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus aviarius

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769708_bin.1_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769641 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus aviarius

characteristic: organism

text: Ligilactobacillus aviarius

text: multi-marker approach

text: Binned metagenome: ERR6769641_bin.4_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769767 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Escherichia coli

characteristic: project name

characteristic: sample derived from

text: Escherichia coli

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769767_bin.3_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889849 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: uncultured Anaeromassilibacillus sp.

characteristic: organism

text: uncultured Anaeromassilibacillus sp.

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Oscillospiraceae;g__Anaeromassilibacillus;s__

text: multi-marker approach

text: Binned metagenome: ERR6889849_bin.33_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769719 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: Escherichia coli

characteristic: project name

characteristic: sample derived from

text: Escherichia coli

characteristic: sequencing method

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6769719_bin.1_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

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

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769692 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Ligilactobacillus salivarius

characteristic: organism

text: Ligilactobacillus salivarius

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus;s__Ligilactobacillus salivarius

text: multi-marker approach

text: Binned metagenome: ERR6769692_bin.2_MetaWRAP_v1.1_bin

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF COPENHAGEN

text: public

text: not provided

text: MetaWRAP v1.1

text: Chicken digestive system

text: EMG broker account, EMBL-EBI

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6889850 of study ERP131894.

text: Ileum

characteristic: environmental medium

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: chicken gut metagenome

text: Digestive tube

characteristic: local environmental context

text: chicken gut metagenome

characteristic: metagenomic source

text: uncultured Lachnospiraceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Lachnospiraceae bacterium

characteristic: sequencing method

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Eubacteriales;f__Lachnospiraceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Binned metagenome: ERR6889850_bin.1_MetaWRAP_v1.1_bin


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF COPENHAGEN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: not provided

characteristic: assembly software

characteristic: binning parameters

text: MetaWRAP v1.1

characteristic: binning software

text: Chicken digestive system

characteristic: broad-scale environmental context

text: EMG broker account, EMBL-EBI

characteristic: broker name

text: CheckM

text: This sample represents a binned metagenome assembled from the metagenomic run ERR6769785 of study ERP131894.

characteristic: description

text: Ileum

text: Spain

text: metagenome-assembled genome

text: chicken gut metagenome

text: Digestive tube

text: chicken gut metagenome

text: Limosilactobacillus vaginalis

characteristic: organism

text: Metagenomic raw reads, assemblies, and bins derived from HoloFood chicken ileum samples. Samples selected for this batch were deeply sequenced, and were randomised among trials (feed), age, and breed to overcome batch effect. The samples in this project contributed to the chicken ileum MAG catalogue (project: PRJEB55375 [ERP140264]).

text: Limosilactobacillus vaginalis

text: The taxonomy of this binned metagenome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus;s__Limosilactobacillus vaginalis

text: multi-marker approach

text: Binned metagenome: ERR6769785_bin.10_MetaWRAP_v1.1_bin

characteristic: title