status: PUBLIC

text: Actinarctus sp.

tag: attribute

characteristic: ArrayExpress-SPECIES

characteristic: ENA first public

characteristic: ENA last update

characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center alias

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Actinarctus sp.

characteristic: common name

text: unidentified

characteristic: organism

characteristic: subject id

text: Actinarctus sp.

characteristic: title


text: Caenorhabditis brenneri

text: SC

text: Wellcome Sanger Institute

text: public

text: Caenorhabditis brenneri

text: Caenorhabditis brenneri

text: Caenorhabditis brenneri


text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

tag: Namespace:CURTIN UNIVERSITY

characteristic: collection date

text: Beef abattoir

characteristic: environment (biome)

text: Boning room

characteristic: environment (feature)

text: Processing line

characteristic: environment (material)

text: Australia

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

text: Microbial contamination through boning in Australian beef export abattoirs

characteristic: project name

text: Illumina MiSeq

characteristic: sequencing method

text: Pre-chill carcase


characteristic: ENA first public

characteristic: ENA last update

characteristic: ENA-CHECKLIST

characteristic: External Id

text: CURTIN UNIVERSITY

characteristic: INSDC center alias

text: CURTIN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Beef abattoir

text: Boning room

text: Chiller

text: Australia

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Post-chill carcase


text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

characteristic: Submitter Id

characteristic: collection date

text: Beef abattoir

characteristic: environment (biome)

text: Boning room

characteristic: environment (feature)

text: Processing line

characteristic: environment (material)

text: Australia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenome

characteristic: organism

text: Illumina MiSeq

text: Forequarter carcase

characteristic: title


characteristic: ENA first public

characteristic: ENA last update

text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

text: Beef abattoir

text: Boning room

text: Processing line

text: Australia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

characteristic: miscellaneous environmental package

text: metagenome

characteristic: project name

text: Illumina MiSeq

characteristic: sequencing method

text: Hindquarter carcase


characteristic: ENA-CHECKLIST

characteristic: External Id

text: CURTIN UNIVERSITY

characteristic: INSDC center alias

text: CURTIN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Beef abattoir

text: Boning room

text: Boning stations

text: Australia

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Environmental surface


text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

characteristic: Submitter Id

characteristic: collection date

text: Beef abattoir

characteristic: environment (biome)

text: Boning room

characteristic: environment (feature)

text: Boning table

characteristic: environment (material)

text: Australia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenome

characteristic: organism

text: Illumina MiSeq

text: Beef trim from blade

characteristic: title


characteristic: ENA first public

characteristic: ENA last update

text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

text: Beef abattoir

text: Boning room

text: Boning table

text: Australia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

characteristic: miscellaneous environmental package

text: metagenome

characteristic: project name

text: Illumina MiSeq

characteristic: sequencing method

text: Beef trim from rump


characteristic: ENA-CHECKLIST

characteristic: External Id

text: CURTIN UNIVERSITY

characteristic: INSDC center alias

text: CURTIN UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Beef abattoir

text: Boning room

text: Boning table

text: Australia

text: metagenome

text: metagenome

text: Illumina MiSeq

text: Manufacturing beef


text: CURTIN UNIVERSITY

text: CURTIN UNIVERSITY

text: public

characteristic: Submitter Id

characteristic: collection date

text: Beef abattoir

characteristic: environment (biome)

text: Boning room

characteristic: environment (feature)

text: Boning table

characteristic: environment (material)

text: Australia

characteristic: geographic location (country and/or sea)

text: metagenome

text: metagenome

characteristic: organism

text: Illumina MiSeq

text: Beef trim from brisket

characteristic: title


characteristic: ENA first public

characteristic: ENA last update

text: Georgia State University

text: Georgia State University

text: public

tag: Namespace:Georgia State University

text: house mouse

characteristic: common name

characteristic: description

text: terrestrial biome

text: animal-associated habitat

text: feces

text: USA

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Mus musculus

characteristic: project name

text: Illumina MiSeq

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Umea university

characteristic: INSDC center alias

text: Umea university

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Umea university

characteristic: Submitter Id

text: 6 to 10

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: dendritic cell

characteristic: cell type

text: house mouse

text: Protocols: Post infection, cells were treated with Fc-block (anti-mouse CD16/CD32 antibody, 1:200; BD 553142) for 15 minutes, washed with D-PBS and further incubated with a monoclonal antibody against CD11c conjugated with PE-Cyanine7 (1:200; Thermofisher 25-0114-82) for 30 minutes, washed with D-PBS and resuspended in ice-cold D-PBS. Cells were kept on ice prior to sorting. The sorting was performed with a MoFlo Astrios EQ (Beckman Coulter, USA) cell sorter using a 488 and 532 nm laser for excitation, 100 µm nozzle, sheath pressure of 25 psi and 0.1 µm sterile filtered 1 x PBS as sheath fluid. Flow sorting data was interpreted and displayed using the associated software Summit v 6.3.1. Primary bone marrow-derived dendritic cells (BMDCs) were generated as previously described (Fuks et. al., 2012, Kanatani et. al., 2017). Briefly, cells from bone marrow of 6-10 week old C57BL/6 mice (Charles River) were cultured in RPMI 1640 (Gibco) with 10% fetal bovine serum (FBS, Sigma), gentamicin (20 μg/ml; Gibco), glutamine (2 mM; Gibco) and HEPES (0.01 M; Gibco), referred to as complete medium, and supplemented with 10 ng/ml recombinant mouse GM-CSF (Peprotech). Medium was replenished on days 2,4 and 6. Loosely adherent cells were harvested on day 7/8 for experiments. The parasite lines used include GFP-expressing RH-LDMluc (type I, cloned from RH-GFPS65T) and GFP-expressing PTGluc (type II, cloned from ME49/PTG-GFPS65T). Tachyzoites were maintained by serial 2-day passaging in human foreskin fibroblast (HFF-1 SCRC-1041, American Type Culture Collection) monolayers cultured in Dulbecco‘s modified Eagle’s medium (DMEM; Gibco) with 10% FBS, gentamicin (20μg/ml), glutamine (2mM), and HEPES (0.01 M). Infection challenges, lysates and LPS On day seven or eight, DCs in complete media were challenged with freshly egressed T. gondii tachyzoites for 3 hours at MOI (multiplicity of infection) 3, or 12 hours at MOI 1.5, or treated with parasite lysates or 100ng/ml LPS for 3 hours. The parasite lysates were produced by ultrasonication of live tachyzoites, where ultrasonication was applied 3 times at 10 second intervals with 1-minute intervals on ice. CD11c staining of DCs Post infection, cells were treated with Fc-block (anti-mouse CD16/CD32 antibody, 1:200; BD 553142) for 15 minutes, washed with D-PBS and further incubated with a monoclonal antibody against CD11c conjugated with PE-Cyanine7 (1:200; Thermofisher 25-0114-82) for 30 minutes, washed with D-PBS and resuspended in ice-cold D-PBS. Cells were kept on ice prior to sorting. Individual DCs or T. gondii infected DCs were deposited into 384-well plates (Eppendorf twin.tecTM PCR plates) containing 2.3 µl lysis buffer3 using a CyCloneTM robotic arm and the most stringent single cell sort settings (single mode, 0.5 drop envelope). Side scatter was used as trigger channel and sort regions were based on Toxoplasma cells expressing GFP and the surface antibody CD11C-PE-Cy7 bound to human dendritic cells. GFP was excited at 488 nm and detected with a 530/40 nm bandpass filter whereas PE-Cy7 was excited at 532 nm and detected using a 695/70 nm bandpass filter. The plate and sample holder was kept at 4 ºC at all times during the sort. After the sort, the plates were immediately spun down and put on dry ice. Single dendritic cells or single T. gondii infected dendritic cells were sorted directly into lysis buffer and cDNA libraries were generated by the Eukaryotic Single Cell Genomics Facility at SciLifeLab, Stockholm using Smart-seq2. Smart-seq2

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

characteristic: plate number

characteristic: plate well

text: female

characteristic: sex

characteristic: strain