characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Laboratory of Molecular Biology, Mamatsio General Hospital of Kozani

text: not provided

text: Greece

text: Kozani

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA

characteristic: organism

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:INSTITUTE OF APPLIED BIOSCIENCES - CERTH

text: University General Hospital of Thessaloniki, AHEPA

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Thessaloniki

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: RNA

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUTE OF APPLIED BIOSCIENCES - CERTH

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Theageneio Hospital of Thessaloniki

text: not provided

text: Greece

text: Thessaloniki

text: human

text: not provided

text: Homo sapiens

text: not provided

text: RNA

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

text: public

text: General Hospital of Goumenissa

characteristic: collecting institution

text: not provided

characteristic: collector name

characteristic: common name

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: Goumenissa

characteristic: geographic location (region and locality)

text: human

text: not provided

text: Homo sapiens

text: male

text: RNA


E-MTAB-12376:Gal8-/- 1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Lampix therapeutics

text: public

text: E-MTAB-12376:Gal8-/- 1

tag: Namespace:Lampix therapeutics

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: neutrophil

text: gray mouse lemur

text: Protocols: FACS sorted neutrophils from infected corneas of wild type (WT) or Gal8 knockout (KO). PA infected corneas were harvested from wild type (WT) or Gal8 knockout (KO, Gal-8-/-) mice on day 1 p.i., pooled group wise (20-30 corneas/group), and digested in 200 µl of DMEM containing collagenase and DNase (100 µg/mL each, Roche Diagnostics, Indianapolis, IN) for 45 min at 37°C in a water bath. After incubation, the corneas were disrupted by grinding with a syringe plunger on a cell strainer, and single-cell suspensions were made in complete DMEM medium. For PMN sorting, cells were blocked with an unconjugated anti-CD32/CD16 mAb (clone 2.4G2, 30 min) in staining buffer (2% FBS, 5 mM EDTA in PBS) and then incubated for 30 min at 4°C with a cocktail of: CD45 (Clone 30-F11), CD11b-PerCP (clone M170), and Ly6G (clone 1A8). All antibodies were purchased from BD Bioscience (San Jose, CA). Then cells were washed three times using PBS and incubated with APC-fixable viability dye (1/1000, 30 min, 4°C), washed again and resuspended for FACS sorting on FACS Aria cell sorter (Becton Dickinson). The yield of neutrophils was 1-1.5 x 10^5 cells/20 infected corneas. RNA extracted using Qiagen RAN extraction assay. ® RNA-Seq System (NuGEN Technologies) was used to construct cDNA libraries from total RNA.

text: adult

characteristic: developmental stage

text: primary bacterial infectious disease

characteristic: disease

characteristic: genotype

text: Pseudomonas aeruginosa

characteristic: infect

text: Microcebus murinus

text: Microcebus murinus

text: cornea

characteristic: organism part

characteristic: replicate

text: Microcebus murinus

text: female

characteristic: sex

text: Gal8-/- 1


E-MTAB-12376:Gal8-/- 2

characteristic: ENA-CHECKLIST

characteristic: External Id

text: Lampix therapeutics

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12376:Gal8-/- 2

characteristic: Submitter Id

text: ArrayExpress

text: primary cell line

text: neutrophil

text: gray mouse lemur

text: adult

text: primary bacterial infectious disease

text: Pseudomonas aeruginosa

text: Microcebus murinus

characteristic: organism

text: Microcebus murinus

text: cornea

text: Microcebus murinus

text: female

text: Gal8-/- 2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Lampix therapeutics

text: public

text: ArrayExpress

characteristic: broker name

text: primary cell line

text: neutrophil

text: gray mouse lemur

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: primary bacterial infectious disease

text: wild type genotype

text: Pseudomonas aeruginosa

text: Microcebus murinus

text: Microcebus murinus

text: cornea

text: Microcebus murinus

text: female

text: WT


E-MTAB-12376:WT 2

text: Lampix therapeutics

text: public

text: E-MTAB-12376:WT 2

text: ArrayExpress

text: primary cell line

text: neutrophil

text: gray mouse lemur

text: adult

text: primary bacterial infectious disease

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Pseudomonas aeruginosa

characteristic: infect

text: Microcebus murinus

text: Microcebus murinus

text: cornea

characteristic: organism part

characteristic: replicate

text: Microcebus murinus

text: female

characteristic: sex

text: WT 2


characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Semmelweis University, Department of Pharmacology and Pharmacotherapy

text: 8 to 12

unit: week

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Mice were sacrificed under ketamine/xylazine anaesthesia (100/10 mg/kg), underwent whole-body perfusion with phosphate-buffered saline (PBS) and hearts were stored for molecular analyses after fast freezing in liquid nitrogen. We have used the following anti-PD-1 antibody: Anti-PD-1, 200 ug / mouse, 3 times / week; BioXCell cat.no.: BP0146. For control animals, we have used the following isotype control antibody: Rat IgG2a isotype control, 200 ug / mouse, 3 times / week; BioXCell cat.no.: BP0089 Total RNA was isolated from mouse heart, thymus and spleen samples with a chloroform/isopropanol precipitation method. Briefly, Qiazol® (Qiagen, The Netherlands) was added to each sample and homogenized with TissueLyser (Qiagen, The Netherlands). Homogenates were centrifuged, and from the clean upper phase, DNA and protein were precipitated with chloroform. Total RNA was precipitated with isopropanol, and pellets were washed four times with 75% ethanol (vWR, PA, US). Finally, total RNA was resuspended in nuclease-free water. For Gene Expression Profiling (GEx) library construction, QuantSeq 3‘mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen GmbH, Wien, Austria) was applied according to the manufacturer’s protocol. The quality and quantity of the library was determined by using High Sensitivity DNA1000 ScreenTape system with 2200 Tapestation (Agilent Technologies, Santa Clara, CA, USA) and dsDNA HS Assay Kit with Qubit 3.0 Fluorometer (Thermo Fisher Scientific, Waltham, MA, USA), respectively.

text: adult

text: normal

text: wild type genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: heart

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Semmelweis University, Department of Pharmacology and Pharmacotherapy

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 8 to 12

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: heart

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

tag: Namespace:Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.01 m

unit: m

characteristic: depth

text: deep-sea sediment sample; PC1; 0-1 cm

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: marine abyssal zone biome [ENVO:01000027]

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Alfred-Wegener-Institute Helmholtz-Center for Polar and Marine Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

text: deep-sea sediment sample; PC1; 1-2 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.03 m

text: deep-sea sediment sample; PC1; 2-3 cm

characteristic: description

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


text: public

text: marine benthic biome [ENVO:01000024]

text: 0.04 m

characteristic: depth

text: deep-sea sediment sample; PC1; 3-4 cm

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: marine benthic biome [ENVO:01000024]

text: 0.05 m

text: deep-sea sediment sample; PC1; 4-5 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.01 m

text: deep-sea sediment sample; PC2; 0-1 cm

characteristic: description

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

characteristic: depth

text: deep-sea sediment sample; PC2; 1-2 cm

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.03 m

text: deep-sea sediment sample; PC2; 2-3 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

text: 0.04 m

text: deep-sea sediment sample; PC2; 3-4 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: collection date

text: 0.05 m

characteristic: depth

text: deep-sea sediment sample; PC2; 4-5 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.01 m

text: deep-sea sediment sample; PC3; 0-1 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

text: deep-sea sediment sample; PC3; 1-2 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.03 m

characteristic: depth

text: deep-sea sediment sample; PC3; 2-3 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.04 m

text: deep-sea sediment sample; PC3; 3-4 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.05 m

text: deep-sea sediment sample; PC3; 4-5 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.01 m

characteristic: depth

text: deep-sea sediment sample; PC4; 0-1 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

text: deep-sea sediment sample; PC4; 1-2 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.03 m

text: deep-sea sediment sample; PC4; 2-3 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.04 m

characteristic: depth

text: deep-sea sediment sample; PC4; 3-4 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.05 m

text: deep-sea sediment sample; PC4; 4-5 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.01 m

text: deep-sea sediment sample; PC5; 0-1 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.02 m

characteristic: depth

text: deep-sea sediment sample; PC5; 1-2 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.03 m

text: deep-sea sediment sample; PC5; 2-3 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.04 m

text: deep-sea sediment sample; PC5; 3-4 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.05 m

characteristic: depth

text: deep-sea sediment sample; PC5; 4-5 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.01 m

text: deep-sea sediment sample; PC6; 0-1 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

text: deep-sea sediment sample; PC6; 1-2 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.03 m

characteristic: depth

text: deep-sea sediment sample; PC6; 2-3 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.04 m

text: deep-sea sediment sample; PC6; 3-4 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.05 m

text: deep-sea sediment sample; PC6; 4-5 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.01 m

characteristic: depth

text: deep-sea sediment sample; PC7; 0-1 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.02 m

text: deep-sea sediment sample; PC7; 1-2 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.03 m

text: deep-sea sediment sample; PC7; 2-3 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.04 m

characteristic: depth

text: deep-sea sediment sample; PC7; 3-4 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.05 m

text: deep-sea sediment sample; PC7; 4-5 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.01 m

text: deep-sea sediment sample; PC8; 0-1 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.02 m

characteristic: depth

text: deep-sea sediment sample; PC8; 1-2 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

characteristic: environmental medium

text: Arctic Ocean

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

characteristic: project name

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: marine benthic biome [ENVO:01000024]

text: 0.03 m

text: deep-sea sediment sample; PC8; 2-3 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine benthic biome [ENVO:01000024]

text: 0.04 m

text: deep-sea sediment sample; PC8; 3-4 cm

text: -2433 m

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

text: marine sediment metagenome

characteristic: organism

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome

characteristic: title


text: public

text: marine benthic biome [ENVO:01000024]

characteristic: broad-scale environmental context

characteristic: collection date

text: 0.05 m

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text: deep-sea sediment sample; PC8; 4-5 cm

characteristic: description

text: -2433 m

characteristic: elevation

text: deep marine sediment [ENVO:00002113]

text: Arctic Ocean

characteristic: geographic location (longitude)

characteristic: local environmental context

text: marine sediment metagenome

text: Iron impacted Arctic deep-sea sediments

text: marine sediment metagenome


characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

characteristic: INSDC first public

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text: public

tag: Namespace:BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO

text: freshwater ecosystem

text: Freshwater Jiricka pond metagenome

text: water

characteristic: environmental medium

text: Czech Republic

text: Czech Republic

characteristic: geographic location (region and locality)

text: freshwater lake biome

text: lake water metagenome

characteristic: project name

text: lake water metagenome

text: Illumina Novaseq 6000

characteristic: sequencing method

unit: ºC

characteristic: temperature

text: Freshwater pond metagenome


characteristic: ENA-CHECKLIST

characteristic: External Id

text: BIOLOGY CENTRE ASCR, V.V.I., INSTITUTE OF HYDROBIO

text: public

characteristic: INSDC status

characteristic: SRA accession

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text: freshwater ecosystem

characteristic: broad-scale environmental context

text: Freshwater Jiricka pond metagenome

text: water

text: Czech Republic

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: Czech Republic

text: freshwater lake biome

text: lake water metagenome

characteristic: organism

text: lake water metagenome

text: Illumina Novaseq 6000

text: Freshwater pond metagenome

characteristic: title


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characteristic: ENA-LAST-UPDATE

text: ROSWELL PARK CANCER INSTITUTE

characteristic: INSDC center name

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text: public

tag: Namespace:ROSWELL PARK CANCER INSTITUTE

text: Joseph Barbi group

text: house mouse

characteristic: common name

text: Lung

characteristic: description

text: yes

text: Mus musculus

text: Mus musculus

text: Lung


text: ROSWELL PARK CANCER INSTITUTE

characteristic: INSDC last update

text: public

text: Joseph Barbi group

text: house mouse

text: Lung

text: no

text: Mus musculus

text: Mus musculus

text: Lung


characteristic: ENA-CHECKLIST

text: UNIVERSITY OF OXFORD

text: public

tag: Namespace:UNIVERSITY OF OXFORD

text: University of Oxford

characteristic: collecting institution

characteristic: collection date

text: Modernising Medical Microbiology

characteristic: collector name

text: United Kingdom

text: human

characteristic: host common name

text: not collected

characteristic: host health state

text: Homo sapien

characteristic: host scientific name

text: not collected

characteristic: host sex

text: not collected

characteristic: host subject id

text: RT-PCR

characteristic: influenza test method

text: P

characteristic: influenza test result

text: Influenza A virus

text: Influenza A virus

text: Influenza genome sequencing


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

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tag: Namespace:Dept. Medical Biotechnology and Translational Medicine, University of Milan

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text: ArrayExpress

characteristic: broker name

text: cortical neurons

text: house mouse

text: Protocols: Cortical neurons at Div14 were lysed in Purozol (cod.7326890; Bio-rad) on ice and samples stored at -80°C. Cortical WT neurons were seeded on 6-well plates and cultured in neuronal medium under the influence of WT or Mecp2 KO cortical astrocytes, which were seeded on transwell inserts. When neurons were at Div0, transwell inserts with astrocytes were transferred on cultured cells and the co-cultures were maintained until Div14, without medium supplementation at Div7. Cortical WT neurons were cultivated from Div0 to Div14 under the influence of paracrine factors secreted by Mecp2 KO astrocytes, or WT astrocytes. Neurons cultivated alone were also included. RNA was extracted by using Purezol (cod.7326890; Bio-rad) following . DNasi I Amplification Grade (cod.AMPD1; Sigma-Aldrich) was used to remove eventual genomic DNA contamination and a second RNA extraction was performed in Purezol. RNA integrity was verified using the RNA 6000 Nano Kit on a Bioanalyzer (Agilent Technologies); all samples had a RIN>9. RNA was quantified using Qubit RNA BR Assay Kit. RNA-seq libraries were generated using the TruSeq stranded mRNA kit (Illumina) from 400 ng of RNA samples, after poly(A) capture and according to manufacturer’s instructions. Quality and size of RNAseq libraries were assessed by capillary electrophoretic analysis with the Agilent 4200 Tape station (Agilent). Libraries were quantified by real-time PCR against a standard curve with the KAPA Library Quantification Kit (KapaBiosystems, Wilmington, MA, USA).

text: normal

characteristic: disease

text: wild type genotype

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text: transwell co-culture with Mecp2 -/- astrocytes

characteristic: growth condition

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: cerebral cortex

characteristic: organism part

text: Mus musculus

text: CD1 mus strain

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text: Dept. Medical Biotechnology and Translational Medicine, University of Milan

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text: public

text: ArrayExpress

text: cortical neurons

text: house mouse

characteristic: common name

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text: normal

text: wild type genotype

text: not applicable

text: Mus musculus

text: Mus musculus

text: cerebral cortex

text: Mus musculus

text: CD1 mus strain


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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: cortical neurons

text: house mouse

text: normal

text: wild type genotype

text: transwell co-culture with wild-type astrocytes

text: not applicable

text: Mus musculus

text: Mus musculus

text: cerebral cortex

text: Mus musculus

text: CD1 mus strain


text: public

characteristic: Submitter Id

text: ArrayExpress

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text: cortical neurons

text: house mouse

text: normal

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text: monoculture

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text: not applicable

text: Mus musculus

text: Mus musculus

text: cerebral cortex

text: Mus musculus

text: CD1 mus strain


characteristic: GISAID Accession ID

text: Dr. Risch

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tag: Namespace:Dr. Risch

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text: Labormedizinisches Zentrum Dr. Risch, Liebefeld, Switzerland

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text: Nadia Wohlwend, Faina Wehrli, Dominique Fabien Hilti, Sinem Kas, Martin Risch, Thomas Bodmer, Lorenz Risch

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text: Dr. Risch

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text: Severe acute respiratory syndrome coronavirus 2


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text: Labormedizinisches Zentrum Dr. Risch, Liebefeld, Switzerland

text: Nadia Wohlwend, Faina Wehrli, Dominique Fabien Hilti, Sinem Kas, Martin Risch, Thomas Bodmer, Lorenz Risch

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text: E-MTAB-10902:PCN_Nzip-mutation-reporter_shAgo2_Neurite_1

tag: Namespace:Berlin Institute for Medical Systems Biology (BIMSB) Max Delbruck Center for Molecular Medicine

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text: neuron of cerebral cortex

text: neuron projection

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text: Protocols: Soma samples were collected from top of the filter membrane and neurite samples form the cleaned membranes at DIV9. See also: “Ludwik et al. 2019: Genome-wide analysis of RNA and protein localization and local translation in mESC-derived neurons” Cortical neurons were isolated from E14 and P0 pups and plated on microporous membranes in 6-well plates. Astrocytes were pre-seeded on the 6-well dishes around one week in advance of plating. Cells were cultured as previously described (Kaech & Banker, 2006). Neurons were transfected using lentiviral particles carrying either shRNA expression constructs or GFP constructs with inserts from one of the reporter library pools or. Viral particles were applied onto the neurons between DIV1 and DIV5. After collection samples were immediately transferred into Trizol and RNA extraction was performed according to manufacturer’s instructions (see also Ludwik et al. 2019). 100-200ng of total RNA was reverse transcribed into cDNA with a primer complementary to the 3' adapter flanking the tiles. UMIs were introduced during the second strand synthesis with a pool of primers complementary to the 5' adapter flanking the tiles.

characteristic: description

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text: 4 to 8 individuals from litter11

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text: libraries contain only the Nzip-reporter inserts

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