characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 24h

characteristic: environment (material)

text: France

text: Flavert

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


status: PUBLIC

tag: attribute

text: INRAE Pays de la Loire

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:INRAE Pays de la Loire

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

characteristic: description

text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates pool of all times

text: France

characteristic: geographic location (country and/or sea)

text: Flavert

characteristic: host genotype

text: metagenome

text: plant metagenome

text: SUCSEED project - Seed microbiota of tomato, rapeseed and bean

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene - ITS1

characteristic: target gene

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 2h

characteristic: environment (material)

text: France

text: Contender

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


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characteristic: INSDC center name

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characteristic: common name

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 8h

text: France

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text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

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text: bean

text: Seed exudates

characteristic: description

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characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 16h

text: France

characteristic: geographic location (country and/or sea)

text: Contender

characteristic: host genotype

text: metagenome

text: plant metagenome

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: INRAE Pays de la Loire

text: public

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text: field

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text: Seed exudates 24h

characteristic: environment (material)

text: France

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text: metagenome

text: plant metagenome

text: plant metagenome

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characteristic: target gene

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characteristic: INSDC center name

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text: Seed exudates pool of all times

text: France

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text: metagenome

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text: plant metagenome

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characteristic: Submitter Id

text: bean

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text: Seed exudates

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text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 2h

text: France

characteristic: geographic location (country and/or sea)

text: Deezer

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

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characteristic: Submitter Id

text: bean

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text: plant metagenome

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text: plant metagenome

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characteristic: External Id

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text: France

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characteristic: INSDC center name

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characteristic: SRA accession

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text: Brain sur l Authion - Maine et Loire

text: Seed exudates 2h

text: France

text: Vanilla

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characteristic: project name

text: plant metagenome

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characteristic: Submitter Id

text: bean

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text: Seed exudates

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text: Seed exudates 8h

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text: plant metagenome

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characteristic: target gene

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characteristic: External Id

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text: bean

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text: Seed exudates 16h

characteristic: environment (material)

text: France

text: Vanilla

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characteristic: investigation type

text: plant metagenome

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text: France

characteristic: geographic location (country and/or sea)

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characteristic: host genotype

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text: plant metagenome

text: plant metagenome

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characteristic: Submitter Id

text: bean

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text: Seed exudates

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text: Brain sur l Authion - Maine et Loire

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text: Seed exudates pool of all times

text: France

text: Vanilla

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characteristic: project name

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text: gyrB gene - ITS1


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characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 2h

characteristic: environment (material)

text: France

text: Caprice

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1

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text: INRAE Pays de la Loire

characteristic: INSDC center name

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characteristic: SRA accession

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 8h

text: France

text: Caprice

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

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text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 16h

text: France

characteristic: geographic location (country and/or sea)

text: Caprice

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 24h

characteristic: environment (material)

text: France

text: Caprice

text: metagenome

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characteristic: project name

text: plant metagenome

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text: gyrB gene - ITS1


text: INRAE Pays de la Loire

characteristic: INSDC center name

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text: public

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text: bean

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text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates pool of all times

text: France

text: Caprice

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

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characteristic: target gene

characteristic: title


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

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text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 2h

text: France

text: Facilia

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characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


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characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 8h

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

text: Facilia

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

characteristic: INSDC center name

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text: public

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text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 16h

text: France

text: Facilia

text: metagenome

text: plant metagenome

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

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text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 24h

text: France

text: Facilia

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1

characteristic: target gene

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates pool of all times

characteristic: environment (material)

text: France

text: Facilia

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 2h

text: France

characteristic: geographic location (country and/or sea)

text: Bea Vezer

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

characteristic: description

text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates 8h

text: France

text: Bea Vezer

text: metagenome

text: plant metagenome

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 16h

characteristic: environment (material)

text: France

text: Bea Vezer

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1

characteristic: target gene

characteristic: title


text: INRAE Pays de la Loire

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: bean

text: Seed exudates

text: field

text: Brain sur l Authion - Maine et Loire

text: Seed exudates 24h

text: France

text: Bea Vezer

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Seed exudates

characteristic: description

text: field

characteristic: environment (biome)

text: Brain sur l Authion - Maine et Loire

characteristic: environment (feature)

text: Seed exudates pool of all times

text: France

characteristic: geographic location (country and/or sea)

text: Bea Vezer

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Negative control DNA extraction

text: field

characteristic: environment (material)

text: France

text: metagenome

text: plant metagenome

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene - ITS1


text: INRAE Pays de la Loire

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: bean

text: Positive control DNA extraction

text: field

text: France

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1

characteristic: target gene

characteristic: title


text: INRAE Pays de la Loire

text: public

characteristic: Submitter Id

text: bean

characteristic: common name

text: Negative control PCR

characteristic: description

text: field

characteristic: environment (biome)

characteristic: environment (feature)

text: France

text: metagenome

characteristic: investigation type

text: plant metagenome

characteristic: organism

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

text: public

text: bean

text: Positive control PCR

text: field

characteristic: environment (material)

text: France

characteristic: geographic location (country and/or sea)

characteristic: host genotype

text: metagenome

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene - ITS1


text: IBE(CSIC-UNIVERSITAT POMPEU FABRA)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: eastern gorilla

text: Gorilla beringei

text: Gorilla beringei


text: IBE(CSIC-UNIVERSITAT POMPEU FABRA)

text: public

characteristic: Submitter Id

characteristic: description

text: Nycticebus bengalensis

text: Nycticebus bengalensis

characteristic: title


text: IBE(CSIC-UNIVERSITAT POMPEU FABRA)

text: public

text: Leontopithecus chrysomelas

text: Leontopithecus chrysomelas


text: IBE(CSIC-UNIVERSITAT POMPEU FABRA)

text: public

text: purple-faced leaf monkey

characteristic: common name

text: Trachypithecus vetulus

text: Trachypithecus vetulus


text: public

tag: Namespace:Max Planck Institute for Biology of Ageing

unit: month

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: house mouse

text: Protocols: Liver nuclei (n=4) were prepared from frozen tissue specimens by crushing and dounce homogenising the tissue in 1 ml EZbuffer (SIGMA) (20 strokes with loose and a tight pestle, respectively) and spun 5 min at 300 g. The pellet was incubated on ice for 20 min in EZ-buffer supplemented with DNAseI NEB M0303S (4 units/ml) and 1X DNAseI buffer. Equal volume of EZ-buffer was added and samples were spun 5 min at 500 g and incubated again 10 min on ice in EZ-buffer supplemented with DNAseI NEB M0303S (8 units/ml) and 1X DNAseI buffer. Equal volume of EZ-buffer was added, and samples were spun 5min at 500g, resuspended in NSB (1087.5 µl 1XPBS, 5.5µl 2% BSA, 1.5 µl RNase Inhibitor) and filtered 3 times through a 0.22 µm strainer. For scATAC-seq, 100,000 nuclei were resuspended in 50 µl tagmentation mix. scATAC-seq targeting 4000 cells per sample was performed using a beta version of Chromium Single Cell ATAC Library and Gel Bead kit (10x Genomics, 1000110) according to the manufacturer’s instructions.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: mixed pool of 4 mice

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

text: Old


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Max Planck Institute for Biology of Ageing

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: hepatocyte

text: house mouse

text: adult

text: normal

text: wild type genotype

text: mixed pool of 4 mice

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

text: Young


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: mixed 3 and 18

characteristic: age

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: house mouse

characteristic: common name

text: Protocols: Livers were dissociated using the Miltenyi liver perfusion kit (130-128-030) following the manufacturer’s instructions. For the sc-RNA sequencing experiment the isolated hepatocytes were washed two times with staining buffer (1x PBS, 2mM EDTA, 0.5%BSA) and 1 million hepatocytes were stained with Hoechst (15μg/ml) and Reserpine (5uM) for 30min at 37°C. Dead cells were excluded with PI staining (1μg/ml). Cells were sorted using a BD FACSARIA IIIU or Fusion Cytometer and 130um nozzle. The data were analysed using the BD FACSDiva and FlowJo softwares. part of nucleic acid library construction protocol scRNA-seq libraries were generated using an early version of the Smart-seq3xpress protocol. Reaction conditions were identical to the published final protocol deposited on protocols.io (https://www.protocols.io/view/smart-seq3xpress-yxmvmk1yng3p/v2). Briefly, cells were sorted into 300 nl of lysis buffer containing 0.5 uM oligo-dT primer overlayed with 3 ul Silicon Oil (100 cSt; Sigma-Aldrich). Next, reverse transcription was carried out in 400 nl using 0.75 uM Smart-seq3 TSO. Preamplification of cDNA was performed in 1 ul using SeqAmp polymerase (Takara Bio) for 15 cycles. Subsequently, amplified cDNA was diluted with 9 ul H2O and we used 1 ul for downstream tagmentation using 0.002 ul TDE1 enzyme per cell. Final, indexed libraries were pooled per 384-well plate, cleaned and equimolarly pooled before sequencing.

characteristic: description

text: adult

characteristic: developmental stage

text: normal

text: wild type genotype

text: mixed pool of 4 individuals

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


text: INRAE Pays de la Loire

text: public

text: climatic chamber

characteristic: broad-scale environmental context

characteristic: collection date

text: Inoculum

text: potting mix

characteristic: environmental medium

text: Pseudomonas coleopterorum (8977)

characteristic: experimental factor

text: France

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Flavert

characteristic: host genotype

text: metagenome

characteristic: investigation type

text: small pots

characteristic: local environmental context

text: plant metagenome

characteristic: organism

text: Effect of synthetic community inoculation of bean seeds on seedling microbiota assembly

characteristic: project name

text: plant metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: gyrB gene

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INRAE Pays de la Loire

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: climatic chamber

text: Inoculum

characteristic: description

text: potting mix

text: Lelliottia sp (8978)

text: France

text: Flavert

text: metagenome

text: small pots

text: plant metagenome

text: plant metagenome

text: Illumina MiSeq

text: gyrB gene


text: INRAE Pays de la Loire

text: public

text: climatic chamber

characteristic: broad-scale environmental context

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text: Inoculum

text: potting mix

characteristic: environmental medium

text: Pseudomonas syringae (8979)

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