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text: female

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text: USA

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text: male

text: adult mouth [ENVO:0000165]

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text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3015 week 2 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: male

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3015 week 24 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (latitude)

text: male

characteristic: host sex

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3016 week 0 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: female

characteristic: known pathogenicity

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3016 week 2 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: female

text: adult mouth [ENVO:0000165]

characteristic: local environmental context

text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3016 week 24 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: female

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3095 week 2 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: female

characteristic: host sex

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3103 week 2 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (longitude)

text: female

characteristic: known pathogenicity

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3103 week 24 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: female

text: adult mouth [ENVO:0000165]

characteristic: local environmental context

text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3207 week 0 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

text: female

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3207 week 8 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (latitude)

text: female

characteristic: host sex

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3406 week 0 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (longitude)

text: female

characteristic: known pathogenicity

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3406 week 4 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

text: female

text: adult mouth [ENVO:0000165]

characteristic: local environmental context

text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3502 week 0 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: male

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3502 week 4 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (latitude)

text: male

characteristic: host sex

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3527 week 0 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: female

characteristic: known pathogenicity

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3705 week 0 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: male

text: adult mouth [ENVO:0000165]

characteristic: local environmental context

text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3705 week 2 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: male

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 3705 week 24 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: male

characteristic: host sex

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: RUTGERS UNIVERISTY

text: public

characteristic: SRA accession

text: subject 3775 week 24 saliva sample

text: saliva material [ENVO:02000036]

text: USA

characteristic: geographic location (longitude)

text: female

characteristic: known pathogenicity

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: subject 3929 week 24 saliva sample

text: saliva material [ENVO:02000036]

text: USA

text: female

text: adult mouth [ENVO:0000165]

characteristic: local environmental context

text: human saliva metagenome

characteristic: organism

text: COVID Saliva

text: human saliva metagenome


text: RUTGERS UNIVERISTY

text: public

characteristic: broad-scale environmental context

characteristic: collection date

text: subject 4058 week 0 saliva sample

characteristic: description

text: saliva material [ENVO:02000036]

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

text: female

text: adult mouth [ENVO:0000165]

text: human saliva metagenome

text: COVID Saliva

characteristic: project name

text: human saliva metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

tag: Namespace:Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK -Wellcome Sanger Institute, Cambridge, UK

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: Protocols: Fresh frozen OCT-embedded skin biopsies were cryosectioned as 10 μm sections, placed onto SuperFrost Plus glass slides (Thermo Fisher Scientific, Waltham, MA, USA) and stored for less than a week at -80˚C prior to high sensitivity library preparation. Optimal RNA integrity on the skin sections was assessed by RNAscope using three housekeeping genes with high (UBC) and medium (PPIB) expressors (Supplementary figure 3B). We also validated the integrity of the Visium library after sequencing: all samples presented good RNA quality (Supplementary figure 3C). However, we excluded 2 of the 32 10X Visium samples from further analysis due to poor tissue attachment to the slide. Visium spatial gene expression slides and reagents were used according to manufacturer instructions (10X Genomics). Each capture area (6.5 x 6.5 mm2) contains 5,000 barcoded spots that were 55 μm in diameter (100 μm center to center between spots) providing an average resolution of 1 to 10 cells up to a maximum of 100 cells depending on tissue area. Fresh frozen skin samples were embedded in OCT, cryo-sectioned and processed according to the recommended protocols (Tissue optimization: CG000238; Gene expression: CG000239). Optimal permeabilization time for 10um skin sections was 20minutes. cDNA libraries were quality controlled using the Agilent Bioanalyser. The cDNA libraries were sequenced on the Illumina HiSeq 4000 system, targeting 300 million reads per section with parameters 28cy R1, 8cy i7 index, 0cy i5 index, 91cy read 2.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: temple

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


text: Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK -Wellcome Sanger Institute, Cambridge, UK

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: temple

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: temple

text: Homo sapiens

text: female

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: nose

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: glabella

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: forehead

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: cheek

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: back

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: inguinal part of abdomen

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: abdomen

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: normal

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: thigh

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: pubis

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: body_ inguinal2

characteristic: sample id

text: inguinal part of abdomen

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: basal cell carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: cheek

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: basal cell carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: forehead

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: basal cell carcinoma

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

text: bcc_ face_cheek2

characteristic: sample id

text: cheek

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: basal cell carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: bcc_ face_nose1

text: nose

text: Homo sapiens

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: normal

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: breast

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: scalp

characteristic: sampling site

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: basal cell carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: bcc_ face_nose2

text: nose

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: common name

text: adult

text: basal cell carcinoma

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: skin

text: ear

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: not collected

text: human

text: adult

characteristic: developmental stage

text: basal cell carcinoma

characteristic: disease

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: skin

characteristic: organism part

characteristic: sample id

text: forehead

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: description

text: adult

text: basal cell carcinoma

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

text: nose

text: Homo sapiens

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Georgia State University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Georgia State University

text: house mouse

characteristic: common name

text: terrestrial biome

characteristic: environment (biome)

text: animal-associated habitat

characteristic: environment (feature)

text: feces

characteristic: environment (material)

text: France

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: Mus musculus

text: Illumina MiSeq

characteristic: sequencing method

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:ASST Grande Ospedale Metropolitano Niguarda

characteristic: Submitter Id

characteristic: collection date

text: iGAS

characteristic: description

text: Italy

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not applicable

characteristic: isolate

text: Blood

text: Streptococcus pyogenes

characteristic: organism

text: Streptococcus pyogenes


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ASST Grande Ospedale Metropolitano Niguarda

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: iGAS

text: Italy

text: not applicable

text: Homo sapiens

text: not applicable

text: Blood

text: Streptococcus pyogenes

text: Streptococcus pyogenes


characteristic: ENA-CHECKLIST

text: public

text: iGAS

text: Italy

text: not applicable

text: Homo sapiens

text: not applicable

text: Naso-pharingeal swab

text: Streptococcus pyogenes

text: Streptococcus pyogenes

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: iGAS

text: Italy

text: not applicable

text: Homo sapiens

text: not applicable

text: Purulent material

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: public

characteristic: INSDC status

characteristic: Submitter Id

text: no iGAS

text: Italy

text: not applicable

text: Homo sapiens

text: not applicable

text: Auricular swab

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: public

characteristic: collection date

text: no iGAS

characteristic: description

text: Italy

text: not applicable

text: Homo sapiens

text: not applicable

text: Naso-pharingeal aspirate

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: public

text: no iGAS

text: Italy

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: host health state

text: Homo sapiens

text: not applicable

text: Purulent material

text: Streptococcus pyogenes

text: Streptococcus pyogenes


text: public

text: no iGAS

text: Italy

text: not applicable

text: Homo sapiens

characteristic: host scientific name

text: not applicable

characteristic: isolate

text: Pharingeal swab

text: Streptococcus pyogenes

text: Streptococcus pyogenes


characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:Mario Negri Institute for pharmacological research (IRCCS)

text: 8 to 12

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: smooth muscle cell

text: not collected

text: house mouse

characteristic: common name

text: Protocols: Mice were housed in 12 hour light/dark cycles (7am-7pm) and given ad libitum access to a standard rodent chow diet and water. 8-12-week-old male mice were used in all animal experiments. Mice were kept in the Koc University Animal Research Facility in accordance with institutional policies perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in bioRxiv preprint doi: https://doi.org/10.1101/2023.01.23.525138; this version posted January 23, 2023. The copyright holder for this 9 and animal care ethics guidelines. EDA2R-KO and NIK-floxed mice were generated by Genentech8,29 . NIK-floxed mice were a gift from Prof. Shao-Cong Sun (MD Anderson Cancer Center). Myo-NIK-KO mice were generated by crossing NIK-floxed and ACTA1-Cre mice (Jackson strain #006149). OSMR-floxed mice (strain #011081) were purchased from Jackson laboratory. Myo-OSMR-KO mice were generated by crossing OSMR flox and ACTA1-Cre mice (Jackson strain #006149). All mice were maintained on a pure C57BL/6 background. Plasma CRP levels were measured using an ELISA assay (BT Lab E0218Mo). All animal protocols were approved by the Institutional Animal Care and Use Committee of Koc University. Before library preparation, RNA concentration was evaluated through Qubit™ RNA High Sensitivity Assay Kit (Invitrogen, Walthman, MA, USA) while RNA quality was established using 4200 Tapestation (Agilent Technologies, Santa Clara, CA, USA). Protocol: miRNeasy Mini Kit. Following the TruSeq Stranded Total RNA protocol (Illumina, San Diego, CA, USA), at least 500 ng of RNA whose RIN value was between 7 and 9, were used for RNA sequencing. TruSeq Stranded Total RNA Sample Preparation Guide. Following the TruSeq Stranded Total RNA protocol (Illumina, San Diego, CA, USA), at least 500 ng of RNA whose RIN value was between 7 and 9, were used for RNA sequencing.

text: normal

characteristic: disease

text: EDA2R overexpression

characteristic: genotype

text: not collected

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: smooth muscle

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Mario Negri Institute for pharmacological research (IRCCS)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 8 to 12

text: ArrayExpress

text: smooth muscle cell

text: not collected

text: house mouse

text: normal

text: EDA2R overexpression

text: not collected

text: not applicable

text: Mus musculus

text: Mus musculus

text: smooth muscle

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-LAST-UPDATE

text: public

text: 8 to 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: smooth muscle cell

text: not collected

characteristic: collection date

text: house mouse

characteristic: common name

characteristic: description

text: normal

text: GFP (Ctrl)

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: smooth muscle

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IHU Mediterranee infection

text: public

tag: Namespace:IHU Mediterranee infection

text: human

text: ancient human dental pulp

text: France

text: Homo sapiens

characteristic: organism

text: Homo sapiens


characteristic: External Id

text: Institute of Tropical Medicine

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Institute of Tropical Medicine

text: Strain isolated from faeces in household study, household of index patient 6284/4

text: Democratic Republic of the Congo

text: healthy

characteristic: host health state

text: Human

characteristic: host scientific name

text: Faeces

text: Salmonella enterica subsp. enterica serovar Typhimurium


text: Institute of Tropical Medicine

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Strain isolated from bloodstream infection of index patient 6284/4

text: Democratic Republic of the Congo

text: diseased

text: Human

text: Blood

text: Bloodstream infection_6284/4

characteristic: title


characteristic: ENA-LAST-UPDATE

text: Institute of Tropical Medicine

text: public

characteristic: collection date

text: Strain isolated from bloodstream infection of index patient 5568/4

text: Democratic Republic of the Congo

text: diseased

text: Human

text: Blood

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: Bloodstream infection_5568/4


text: Institute of Tropical Medicine

text: public

text: Strain isolated from faeces in household study, household of index patient 5568/4

characteristic: description

text: Democratic Republic of the Congo

characteristic: geographic location (country and/or sea)

text: healthy

text: Human

text: Faeces


characteristic: ENA-CHECKLIST

text: Robert Koch Institute

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10150-CVDP-2CB8D3B0-8285-412D-98D8-D7233CD13DD7

tag: Namespace:Robert Koch Institute

text: RKI-OSEDA

characteristic: broker name

text: SYNLAB MVZ Weiden, Zur Kesselschmiede 4; 92637 Weiden in der Oberpfalz

characteristic: collecting institution

text: not provided

characteristic: collector name

text: Germany

text: Europe/Germany/Bavaria

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status

text: Molecular surveillance of SARS-CoV-2 in Germany


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

text: IMS-10150-CVDP-8FF3BFB5-AE4A-4689-9D9B-0529C973C0D2

characteristic: Submitter Id

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-D5CF2B59-1A48-4C2E-AF0A-63226CAD47C9

text: RKI-OSEDA

characteristic: broker name

text: Sonic - Labor Staber Nürnberg, Deutschherrnstraße 15-19; 90429 Nürnberg

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Bavaria

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Random sampling

text: IMS-10122-CVDP-7F86DDE6-7B40-4921-B36A-7A5252356D78

text: RKI-OSEDA

text: Limbach - MVZ Clotten Labor Freiburg Labor Dr. Haas Dr. Raif & Kollegen GbR, Merzhauser Str. 112 a; 79100 Freiburg im Breisgau

text: not provided

text: Germany

text: Europe/Germany/Baden-Wurttemberg

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-99DDD9A6-18F9-42FE-8117-27E59114F50F

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: LabKom - Labor Augsburg MVZ GmbH, August-Wessels-Straße 5; 86154 Augsburg

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Suspect sampling

text: IMS-10182-CVDP-5C48942C-60A2-405C-B5DB-5D4349F776BD

text: RKI-OSEDA

text: Labor Becker & Kollegen (Standort München), Führichstraße 70; 81671 München

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Bavaria

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Suspect sampling

text: IMS-10182-CVDP-AB598C76-96E6-4A5F-9D6C-9D6BEFA0A8AE

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10061-CVDP-A5E1E636-29D3-4C66-BCB5-A489FE48227A

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: amedes Medlab Arnold Analytik MVZ GmbH, St.-Benedikt-Str. 3; 97072 Würzburg

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

text: IMS-10061-CVDP-F3DC7A56-78B9-4EA7-8D85-86DF04206AE7

text: RKI-OSEDA

text: amedes MVZ für Laboratoriumsdiagnostik Raubling GmbH, Am Rossfeld 4; 83064 Raubling

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Bavaria

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Random sampling

text: IMS-10061-CVDP-F25AB6D4-A408-44AC-B13F-99C089ACB33E

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10061-CVDP-BF1379E8-A238-4F4B-BC83-8B3687F592DE

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: not provided

text: Germany

text: Europe/Germany/Bavaria

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism

text: active surveillance in response to outbreak

text: Molecular surveillance of SARS-CoV-2 in Germany


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

text: IMS-10383-CVDP-CEF07D2E-A444-4629-8290-C4A6C6CBD4A4

text: RKI-OSEDA

text: Uniklinikum Regensburg; Institut für klinische Mikrobiologie und Hygiene, Franz-Josef-Strauß-Allee 11; 93053 Regensburg

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Bavaria

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

text: IMS-10013-CVDP-B7811EF2-8A1B-41B5-AF52-046A33C3F5DE

text: RKI-OSEDA

text: Sonic - MVZ Medizinisches Labor Bremen GmbH, Haferwende 12; 28357 Bremen

text: not provided

text: Germany

text: Europe/Germany/Bremen

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-472D4AF4-4BCA-4334-A661-96C864A8E141

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: not provided

text: Germany

text: Europe/Germany/Bremen

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

text: IMS-10013-CVDP-5D7B4B56-E06D-4B96-9524-A5378A40976B

text: RKI-OSEDA

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Bremen

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Random sampling

text: IMS-10338-CVDP-CCFD0A9B-8414-4D3F-B55D-0E4FC57F481A

text: RKI-OSEDA

text: IMD Labor Frankfurt, Heidelberger Str. 13; 60327 Frankfurt am Main

text: not provided

text: Germany

text: Europe/Germany/Hesse

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-DD92367C-E13E-4380-856F-5CE0E2BCFDFA

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: Sonic - Labor Staber MVZ Kassel, Herkulesstr. 34 A; 34119 Kassel

text: not provided

text: Germany

text: Europe/Germany/Hesse

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

text: IMS-10338-CVDP-368DC65A-0437-43AA-91D2-EC8147AF26B9

text: RKI-OSEDA

text: Labormedizin Darmstadt, Rheinstr. 44-46; 64283 Darmstadt

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Hesse

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

text: IMS-10338-CVDP-C1E5C1B5-17FE-4214-A022-E8746D592737

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Hesse

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-EC9E5E94-6026-4A32-99C7-4BB2D1DBB582

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: Sonic - Labor Dr. von Froreich GmbH, Großmoorbogen 25; 21079 Hamburg

text: not provided

text: Germany

text: Europe/Germany/Hamburg

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

text: IMS-10013-CVDP-A21A261E-B6EE-45CB-AAAD-C39542D8C079

text: RKI-OSEDA

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Hamburg

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

text: active surveillance in response to outbreak

text: Molecular surveillance of SARS-CoV-2 in Germany

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: Random sampling

text: IMS-10013-CVDP-D280B77C-C310-4D99-9B57-AA89AC4FB1CB

text: RKI-OSEDA

text: Bioscientia Labor Wermsdorf, Am Fasanenholz 31; 04779 Wermsdorf

text: not provided

text: Germany

text: Europe/Germany/Saxony

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10013-CVDP-64ADDA35-B71A-4D0E-B70C-ADD8075702DD

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

text: not provided

text: Germany

text: Europe/Germany/Saxony

text: Human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: organism


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Random sampling

text: IMS-10150-CVDP-5810FB56-E4D3-48E8-9443-56505A837426

text: RKI-OSEDA

text: SYNLAB MVZ Leinfelden-Echterdingen, Nikolaus-Otto-Str. 6; 70771 Leinfelden-Echterdingen

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Baden-Wurttemberg

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Robert Koch Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

text: IMS-10116-CVDP-6A836977-3B22-40FC-836D-3143EEFC2ECE

text: RKI-OSEDA

text: MVZ Labor Dr. Limbach & Kollegen GbR, Im Breitspiel 15; 69126 Heidelberg

text: not provided

text: Germany

text: Europe/Germany/Baden-Wurttemberg

text: Human

characteristic: host common name

text: not provided

text: Homo sapiens

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: IHU Mediterranee infection

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: human

characteristic: common name

characteristic: description

text: France

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: not provided

characteristic: collection date

text: malaria parasite P. falciparum

text: not provided

characteristic: geographic location (country and/or sea)

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: title


text: INRAE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: France

text: Toulouse

characteristic: geographic location (region and locality)

text: Sus scrofa domesticus

characteristic: host scientific name

text: A1 (huile tournesol 5%)

text: 43.362N 1.22E

text: pig gut metagenome

text: pig gut metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: INRAE

characteristic: INSDC center name

text: public

text: France

text: Toulouse

text: Sus scrofa domesticus

text: A2 (huile tournesol + FB1)

text: 43.362N 1.22E

text: pig gut metagenome

text: pig gut metagenome


text: INRAE

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ZymoBIOMICS Microbial Community DNA Standard. Theoretical Composition Based on Genomic DNA: Listeria monocytogenes - 12%, Pseudomonas aeruginosa - 12%, Bacillus subtilis - 12%, Escherichia coli - 12%, Salmonella enterica - 12%, Lactobacillus fermentum - 12%, Enterococcus faecalis - 12%, Staphylococcus aureus - 12%, Saccharomyces cerevisiae - 2%, and Cryptococcus neoformans - 2%.

text: France

text: pig gut metagenome

text: pig gut metagenome

text: DNA control Mock ZymoBiomics


text: INRAE

text: public

text: ZymoBIOMICS Microbial Community Standard. Theoretical Composition Based on Genomic DNA: Listeria monocytogenes - 12%, Pseudomonas aeruginosa - 12%, Bacillus subtilis - 12%, Escherichia coli - 12%, Salmonella enterica - 12%, Lactobacillus fermentum - 12%, Enterococcus faecalis - 12%, Staphylococcus aureus - 12%, Saccharomyces cerevisiae - 2%, and Cryptococcus neoformans - 2%.

characteristic: description

text: France

text: pig gut metagenome

characteristic: organism

text: pig gut metagenome

text: microbial control Mock ZymoBiomics


E-MTAB-13103:Sample 1

characteristic: ENA-CHECKLIST

text: LabMedMolGe

text: public

text: E-MTAB-13103:Sample 1

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: Protocols: Human colorectal adenocarcinoma cell lines DLD-1, were provided and grown as previously described [Proto et al., 2017; Notarnicola et al., 2008]. When indicated 48 hours before stimulation, growing cells at 70% confluence were made quiescent using phenol red-free RPMI medium containing 0.1% charcoal-stripped serum (CSS), penicillin (100 U/ml) and streptomycin (100 U/ml). The hEGF (Sigma Aldrich, St. Louis, Missouri, USA) was used at 100 ng/ml. The EGFR tyrosine kinase inhibitor, ZD1839, (Selleckem, Planegg, Germany) was used at 2 �M. The EGF neutralizing antibody (10605-R001; Sino Biological, Beijing, China) was used at 1,5 �g/ml. DLD-1-pEGFP and DLD-1-pEGFP_hRIZ2 cells were counted by the method of optical microscopy in the B�rker chamber. DLD-1-pEGFP_hRIZ2 cells were compared with DLD-1-pEGFP cells. total RNAs concentration was measured using RNA HS kit on a Qubit fuorimeter (Life Technologies, Monza, Italy) while its quality and integrity assessed with the Agilent 4200 Tapestation System (Agilent Technologies, Milan, Italy). For RNA sequencing experiments, indexed libraries were prepared using 500 ng of total RNA as starting material using the Illumina Stranded Total RNA prep Ligation with Ribo-Zero Plus kit (Illumina Inc., San Diego, CA, USA).

text: colon adenocarcinoma

characteristic: disease

text: control

characteristic: genetic modification

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: colon

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: Sample 1


E-MTAB-13103:Sample 2

characteristic: ENA-LAST-UPDATE

text: LabMedMolGe

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13103:Sample 2

text: ArrayExpress

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: colon adenocarcinoma

text: control

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-13103:Sample 3

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: LabMedMolGe

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-13103:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: colon adenocarcinoma

text: control

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: Sample 3


E-MTAB-13103:Sample 4

characteristic: ENA-CHECKLIST

text: LabMedMolGe

text: public

text: E-MTAB-13103:Sample 4

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: colon adenocarcinoma

characteristic: disease

text: RIZ2 overexpression

characteristic: genetic modification

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: colon

text: Homo sapiens

text: Sample 4


E-MTAB-13103:Sample 5

characteristic: ENA-LAST-UPDATE

text: LabMedMolGe

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13103:Sample 5

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: colon adenocarcinoma

text: RIZ2 overexpression

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: colon

characteristic: organism part

characteristic: replicate

text: Homo sapiens

text: Sample 5


E-MTAB-13103:Sample 6

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: LabMedMolGe

text: public

characteristic: SRA accession

text: E-MTAB-13103:Sample 6

text: ArrayExpress

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: colon adenocarcinoma

text: RIZ2 overexpression

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colon

text: Homo sapiens

text: Sample 6

characteristic: title


characteristic: ENA-CHECKLIST

text: EURAC Research

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:EURAC Research

characteristic: Submitter Id

text: Eurac

text: human

text: shotgun

characteristic: description

text: Italy

text: South Tyrol, Malles

characteristic: geographic location (region and locality)

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XY

characteristic: sex

text: bone


characteristic: ENA-LAST-UPDATE

text: EURAC Research

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Eurac

text: human

characteristic: common name

text: Italy

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: XY

text: bone


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: EURAC Research

text: public

text: Eurac

text: human

text: shotgun

text: Italy

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XX

text: bone


text: EURAC Research

text: public

characteristic: SRA accession

text: Eurac

characteristic: collection date

text: human

text: nuclear capture 1.24 K

text: Italy

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XX

text: bone


text: EURAC Research

text: public

text: Eurac

text: human

text: nuclear capture 1.24 K

text: Italy

characteristic: geographic location (country and/or sea)

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XY

text: bone

characteristic: title


characteristic: ENA-CHECKLIST

text: EURAC Research

characteristic: INSDC center name

text: public

text: Eurac

text: human

text: mtDNA capture (Coia et al. 2022)

text: Italy

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XX

text: bone


text: EURAC Research

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Eurac

text: human

text: mtDNA capture (Coia et al. 2022)

text: Italy

text: South Tyrol, Malles

text: 46.68646, 10.55027

text: Homo sapiens

text: Homo sapiens

text: XY

text: bone


text: University of Exeter

text: public

tag: Namespace:University of Exeter

text: University of Exeter

text: University of Exeter

characteristic: collecting institution

text: European lobster

characteristic: description

text: United Kingdom

text: Cornwall, Newlyn

characteristic: geographic location (region and locality)

text: coastal

characteristic: habitat

text: adult

characteristic: lifestage

text: Homarus gammarus

text: muscle from crusher claw

characteristic: organism part

text: AquaLeap

characteristic: project name

text: Homarus gammarus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Exeter

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: University of Exeter

text: University of Exeter

text: European lobster

characteristic: common name

text: Homarus gammarus genome assembly

text: United Kingdom

text: Cornwall, Newlyn

text: coastal

text: adult

text: Homarus gammarus

characteristic: organism

text: muscle from crusher claw

text: AquaLeap

text: Homarus gammarus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

tag: Namespace:Interfacutly Bioinformatics Unit, Unversity of Bern

text: 30 to 44

unit: day

characteristic: age

text: Large white

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: bronchiolar epithelial cell

text: not collected

characteristic: collection date

text: pig

text: Protocols: At 24 or 48 hours p.i., the cells were washed twice and cells were lysed using TRIzol Reagent (Life Technologies). The T3 porcine bronchiolar epithelial cell line was generated by InSCREENeX GmbH (Braunschweig, Germany) and kindly provided by Sasha Trapp (Institut national de la recherche agronomique, INRA, France). The cells were maintained at 37°C and 5% CO2 in porAEC medium with supplement (InSCREENeX, INS-ME-1024) in collagen-coated (InSCREENeX, INS-SU-1017) flasks Cells grown in 24-well cell culture plates were inoculated with virus using an MOI of 1 TCID50/cell. Poly I:C was used at a concentration 1/10000. Following an incubation for 90 minutes at 37°C, the inoculum was removed, the cells washed three times with PBS, and fresh porAEC medium added, then cells were returned to the CO2 incubator at 37°C. RNA was extracted using NucleoSpin RNA (Macherey Nagel cat# 740955.50). Library preparation was performed using BRB-Seq library preparation kit (Alithea genomics, PN 10813) following manufacturer’s instruction.

text: juvenile stage

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: mixed

characteristic: individual

text: mixed

characteristic: infect

text: not applicable

characteristic: isolate

text: Sus scrofa

text: Sus scrofa

text: lung

text: Sus scrofa

text: library

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:University of Tartu

characteristic: Submitter Id

characteristic: broad-scale environmental context

unit: m

characteristic: depth

text: pool of 40 soil samples (5 cm diam. cores, 5 cm depth)

characteristic: description

characteristic: elevation

characteristic: environmental medium

text: Estonia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

characteristic: organism

text: The Global Soil Mycobiome consortium dataset

characteristic: project name

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: Colombia

characteristic: geographic location (country and/or sea)

text: soil metagenome

text: soil metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: Brazil

text: soil metagenome

text: soil metagenome


text: University of Tartu

text: public

characteristic: depth

characteristic: description

characteristic: elevation

characteristic: environmental medium

text: Chile

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: Latvia

text: soil metagenome

characteristic: organism

characteristic: project name

text: soil metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Morocco

characteristic: geographic location (country and/or sea)

text: soil metagenome

text: soil metagenome

characteristic: title


text: University of Tartu

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: depth

characteristic: description

characteristic: elevation

characteristic: environmental medium

text: Australia

characteristic: geographic location (latitude)

text: soil metagenome

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: Papua New Guinea

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

text: soil metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Malaysia

text: soil metagenome

characteristic: organism

characteristic: project name

text: soil metagenome


text: University of Tartu

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: depth

characteristic: description

characteristic: elevation

text: Sweden

characteristic: geographic location (country and/or sea)

text: soil metagenome

text: soil metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

characteristic: environmental medium

text: Finland

characteristic: geographic location (latitude)

text: soil metagenome

text: soil metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Norway

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

text: soil metagenome


text: University of Tartu

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: depth

characteristic: description

characteristic: elevation

text: Viet Nam

text: soil metagenome

characteristic: organism

characteristic: project name

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: India

characteristic: geographic location (country and/or sea)

text: soil metagenome

text: soil metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: environmental medium

text: Portugal

characteristic: geographic location (latitude)

text: soil metagenome

text: soil metagenome


text: University of Tartu

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: depth

characteristic: description

characteristic: elevation

text: Italy

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: Switzerland

text: soil metagenome

characteristic: organism

characteristic: project name

text: soil metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Tartu

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Estonia

characteristic: geographic location (country and/or sea)

text: soil metagenome

text: soil metagenome

characteristic: title


text: University of Tartu

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

characteristic: depth

characteristic: description

characteristic: elevation

characteristic: environmental medium

text: Thailand

characteristic: geographic location (latitude)

text: soil metagenome

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Tartu

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: collection date

text: Colombia

characteristic: geographic location (longitude)

characteristic: local environmental context

text: soil metagenome

text: soil metagenome