text: ETH Zurich, DBSSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12004:B7_WTC_KUCG2_HES1_H1_day19_ATAC

characteristic: Submitter Id

text: ArrayExpress

text: 201B7, GM25256, HPSI0214i-kucg_2, H1-hESC, HES-3

text: human

text: normal

text: wild type genotype, PAX6YFP (H1-hESC), NKX2.1GFP (HES-3)

text: cerebral organoid culture

text: Homo sapiens

text: Homo sapiens

text: skin, inner cell mass

text: induced pluripotent stem cell, embryonic stem cell

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ETH Zurich, DBSSE

text: public

text: E-MTAB-12004:Day15_B7_WTC_409B2_WIBJ2_HOIK1_RNA

tag: Namespace:ETH Zurich, DBSSE

text: ArrayExpress

characteristic: broker name

text: 201B7, GM25256, 409B2, HPSI0314i-hoik_1, HPSI0214i-wibj_2

text: human

characteristic: common name

text: Protocols: Single cell suspensions were acquired by dissociation of the organoids with a papain-based dissociation (Miltenyi Biotec, 130-092-628). For 19 days of development, cerebral organoids were generated from five different stem cell lines: three human induced pluripotent stem cell lines 201B7 (B7), GM25256 (WTC), HPSI0214i-kucg_2 (Kucg2), and two human embryonic stem cell line H1-hESC (H1), HES-3 simultaneously. The genotype was PAX6YFP for H1 cells, and NKX2.1GFP for HES-3 cells. For 15 days of development, cerebral organoids were generated from five human induced pluripotent stem cell lines 201B7 (B7), GM25256 (WTC), 409B2, HPSI0314i-hoik_1 (Hoik1), HPSI0214i-wibj_2 (Wibj2). Cerebral organoids were generated using a whole brain organoid differentiation protocol (Lancaster et al. 2013). For scATAC-seq, nuclei were isolated according to the protocol provided by 10x genomics (Demonstrated protocol CG000169 Rev D) using the low input protocol and a lysis time of 3 min. Nuclei were loaded in a concentration that would result in a recovery of 10,000 nuclei. In case of less nuclei recovered, the maximum number of nuclei was targeted. For sc-RNAseq, cells were put in a concentration after counting and viability checking that allowed targeting 10,000 cells and in case the cell number was not sufficient all cells were loaded. After dissociation, cell viability was checked, cells were counted and 7000 cells were targeted per lane of the 10x microfluidic chip. Single cell ATACseq libraries were generated with the Chromium Single Cell ATAC V1 Library & Gel Bead Kit. Single cell RNAseq libraries were generated with the Chromium Single Cell 3’ V3 Library & Gel Bead Kit and sequenced on Illumina’s HiSeq platform.

characteristic: description

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: cerebral organoid culture

characteristic: growth condition

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: skin

characteristic: organism part

text: induced pluripotent stem cell

characteristic: progenitor cell type

text: Homo sapiens

characteristic: title


text: ETH Zurich, DBSSE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12004:B7_WTC_KUCG2_HES1_H1_day19_RNA

text: ArrayExpress

text: human

text: normal

text: cerebral organoid culture

text: Homo sapiens

text: Homo sapiens

text: skin, inner cell mass

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Middle East Technical University

text: public

characteristic: SRA accession

tag: Namespace:Middle East Technical University

characteristic: Submitter Id

text: Archaeological

text: human

text: Human remains

text: Greece

characteristic: geographic location (country and/or sea)

text: METU

text: Homo sapiens

text: Homo sapiens

text: Male

characteristic: sex

text: Petrous Bone


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Middle East Technical University

text: public

text: Archaeological

text: human

characteristic: common name

text: Human remains

characteristic: description

text: Greece

text: METU

text: Homo sapiens

text: Homo sapiens

text: Female

text: Petrous Bone


text: Middle East Technical University

text: public

text: Archaeological

text: human

text: Human remains

text: Georgia

text: METU

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Male

text: Petrous Bone


text: Middle East Technical University

text: public

text: Archaeological

text: human

text: Human remains

text: Georgia

text: METU

text: Homo sapiens

text: Homo sapiens

text: Female

text: Petrous Bone


text: RIVM

text: public

characteristic: collection date

text: mecC-positive MRSA

text: Netherlands

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human purulent material

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Homo sapiens

text: Human wound

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: RIVM

text: public

characteristic: INSDC status

characteristic: SRA accession

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Homo sapiens

text: Human other

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


characteristic: ENA-LAST-UPDATE

text: RIVM

text: public

characteristic: Submitter Id

text: mecC-positive MRSA

text: Netherlands

characteristic: geographic location (country and/or sea)

text: not provided

text: Homo sapiens

text: Human perineum swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


characteristic: External Id

text: RIVM

text: public

text: mecC-positive MRSA

characteristic: description

text: Netherlands

text: not provided

text: Homo sapiens

text: Human urine

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

text: public

characteristic: collection date

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Homo sapiens

text: Human blood

text: Staphylococcus aureus

characteristic: organism

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

text: public

text: mecC-positive MRSA

text: Netherlands

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: Human nose and throat swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

characteristic: INSDC center name

text: public

text: mecC-positive MRSA

text: Netherlands

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text: Human nose swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Homo sapiens

text: Human throat swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


characteristic: ENA-CHECKLIST

text: RIVM

text: public

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Homo sapiens

text: Human nose, perineum and throat swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: RIVM

text: public

characteristic: INSDC status

text: mecC-positive MRSA

text: Netherlands

text: not provided

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text: Human sputum

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


characteristic: ENA-LAST-UPDATE

text: RIVM

text: public

characteristic: SRA accession

text: mecC-positive MRSA

text: Netherlands

text: not provided

text: Erinaceus europaeus

text: Hedgehog nose swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


text: RIVM

text: public

characteristic: Submitter Id

text: mecA-positive MRSA

text: Netherlands

characteristic: geographic location (country and/or sea)

text: not provided

text: Erinaceus europaeus

text: Hedgehog nose swab

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Methicilin resistant isolate


characteristic: External Id

unit: last

characteristic: Further Details

text: University of Oslo

text: public

tag: Namespace:University of Oslo

text: temperate broadleaf forest biome (ENVO_01000202)

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: temperate deciduous broadleaf forest (ENVO_01000385)

characteristic: local environmental context

text: uncultured eukaryote

text: CCAGCA[GC]C[CT]GCGGTAATTCC ACTTTCGTTCTTGAT[CT][AG]A

characteristic: pcr primers

text: uncultured eukaryote

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text: Molde plot 1 Birch Zone LFH


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

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text: Yes

text: Norway

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text: Molde plot 1 Birch Zone M1

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text: University of Oslo

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text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

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text: Molde plot 1 Birch Zone M2


characteristic: Further Details

text: University of Oslo

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text: Yes

text: Norway

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: Molde plot 2 Spruce Zone LFH


characteristic: ENA-FIRST-PUBLIC

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text: Yes

text: Norway

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text: forest soil (ENVO_00002261)

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text: Yes

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text: Norway

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

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text: Molde plot 3 Birch Zone M2


characteristic: ENA-FIRST-PUBLIC

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text: University of Oslo

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text: Norway

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text: uncultured eukaryote

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characteristic: Further Details

text: University of Oslo

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

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text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

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text: Molde plot 4 Spruce Zone M1


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characteristic: ENA-FIRST-PUBLIC

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text: University of Oslo

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text: Yes

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characteristic: geographic location (latitude)

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text: uncultured eukaryote

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text: Molde plot 4 Spruce Zone M3


characteristic: Further Details

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characteristic: environmental medium

text: Yes

text: Norway

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text: uncultured eukaryote

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text: Molde plot 5 Birch Zone M1


characteristic: ENA-FIRST-PUBLIC

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text: University of Oslo

text: public

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text: University of Oslo

text: public

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characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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text: uncultured eukaryote

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characteristic: ENA-CHECKLIST

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text: Stranda plot 1 Birch Zone LFH


characteristic: ENA-FIRST-PUBLIC

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text: University of Oslo

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text: Stranda plot 1 Birch Zone M1


characteristic: Further Details

text: University of Oslo

text: public

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characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

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text: Norway

characteristic: geographic location (latitude)

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text: uncultured eukaryote

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text: Stranda plot 1 Birch Zone M3


characteristic: ENA-FIRST-PUBLIC

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text: Stranda plot 2 Spruce Zone LFH


characteristic: Further Details

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text: Yes

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characteristic: geographic location (country and/or sea)

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characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured eukaryote

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characteristic: Further Details

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characteristic: broad-scale environmental context

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characteristic: environmental medium

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text: Norway

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text: Stranda plot 3 Birch Zone M1


characteristic: ENA-FIRST-PUBLIC

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characteristic: Further Details

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text: public

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characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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text: uncultured eukaryote

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text: Stranda plot 4 Spruce Zone LFH


characteristic: ENA-FIRST-PUBLIC

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text: University of Oslo

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text: Stranda plot 4 Spruce Zone M1


characteristic: Further Details

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characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

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text: Norway

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: ENA-FIRST-PUBLIC

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characteristic: External Id

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text: public

characteristic: INSDC status

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text: Norway

characteristic: local environmental context

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text: Stranda plot 5 Birch Zone LFH


characteristic: Further Details

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characteristic: Submitter Id

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text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

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text: Norway

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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characteristic: Further Details

text: University of Oslo

text: public

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: local environmental context

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text: Stranda plot 6 Spruce Zone LFH


characteristic: ENA-CHECKLIST

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characteristic: collection date

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text: Norway

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text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: JolsterII plot 3 Birch Zone M1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: JolsterII plot 3 Birch Zone M2


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (latitude)

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: JolsterII plot 3 Birch Zone M3


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: uncultured eukaryote

text: JolsterII plot 4 Spruce Zone LFH

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: JolsterII plot 4 Spruce Zone M1


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: JolsterII plot 4 Spruce Zone M2


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: JolsterII plot 4 Spruce Zone M3


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: uncultured eukaryote

text: Molde plot 7 Spruce Zone LFH

characteristic: title


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: Molde plot 7 Spruce Zone M1


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: Molde plot 7 Spruce Zone M2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (latitude)

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: Molde plot 7 Spruce Zone M3


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: uncultured eukaryote

text: JolsterII plot 6b Spruce Zone LFH

characteristic: title


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: JolsterII plot 6b Spruce Zone M1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: JolsterII plot 6b Spruce Zone M2


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

characteristic: geographic location (latitude)

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: JolsterII plot 6b Spruce Zone M3


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: uncultured eukaryote

text: JolsterII plot 5b Birch Zone LFH

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote

text: JolsterII plot 5b Birch Zone M1


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

characteristic: environmental medium

text: Yes

text: Norway

text: uncultured eukaryote

text: uncultured eukaryote

characteristic: target gene

characteristic: target subfragment

text: JolsterII plot 5b Birch Zone M2


characteristic: ENA-CHECKLIST

text: University of Oslo

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: uncultured eukaryote

characteristic: organism

text: uncultured eukaryote

text: JolsterII plot 5b Birch Zone M3


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Oslo

text: public

characteristic: INSDC status

characteristic: collection date

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: geographic location (longitude)

text: uncultured eukaryote

text: uncultured eukaryote


characteristic: Further Details

text: University of Oslo

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: temperate coniferous forest biome (ENVO_01000211)

characteristic: broad-scale environmental context

text: forest soil (ENVO_00002261)

text: Yes

text: Norway

characteristic: local environmental context

text: uncultured eukaryote

characteristic: pcr primers

text: uncultured eukaryote


E-MTAB-12040:Sample 1

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12040:Sample 1

tag: Namespace:Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen  Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen  Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen  Department of Clinical Biochemistry, Bispebjerg & Frederiksberg Hospitals, University of Copenhagen

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: Protocols: The mice were fasted overnight (11 hours) prior to liver isolation, and livers were kept at -80°C until analysis. For eight weeks, female C57BL/6JRj mice (seven weeks old at the start of treatment) received, by subcutaneous injections, either a long-acting glucagon analogue (GCGA, NNC9024-0043, 1.5 nmol/kg body weight, terminal half-life: 5-6 hours) or PBS + 1% BSA (PBS). Dose and administration frequency of GCGA was determined in a pilot study, in which 3 nmol/kg or 30 nmol/kg GCGA or PBS was administered to male and female C57BL/6JRj mice (8 weeks old) once or twice during a 24 hour period. The dose of GCGA was initially 3 nmol/kg body weight, but after 16 days of treatment, one of the mice had lost >20% of its body weight and had to be terminated (this mouse was excluded from the study). Due to this effect of GCGA, the dose was halved (1.5 nmol/kg body weight) for the remainder of the study. Raw sequencing data were processed using bcl2fastq software version 2.20.0 (Illumina). Total DNA/RNA was purified by an AllPrep DNA/RNA Minikit (80204, QIAgen) according to manufacturer’s instructions and quality tested using a 2100 Bioanalyzer instrument (Agilent Genomics). The extract was DNase treated with RNeasy Minikit (74106, QIAgen) and RNase-Free DNase set (79254, QIAgen) according to manufacturer’s protocol. All the above-mentioned processes were performed on a QIACube machine (QIAgen). Library preparation was done using TruSeq Stranded Total RNA Library Prep Gold (20020599, Illumina) and IDT for Illumina-TruSeq RNA UD Indexes (20022371, Illumina) according to the manufacturer’s instructions. Some samples (input <100 ng) were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB-E7760S, New England Biolabs), NEBNext rRNA Depletion Kit 24 with beads (NEB-E7765, New England Biolabs), and NEBNext Multiplex Oligos for Illumina (E7600S, New England Biolabs).

characteristic: description

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 1

characteristic: title


E-MTAB-12040:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen Department of Clinical Biochemistry, Rigshospitalet, University of Copenhagen Department of Clinical Biochemistry, Bispebjerg & Frederiksberg Hospitals, University of Copenhagen

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12040:Sample 2

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 2


E-MTAB-12040:Sample 3

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12040:Sample 3

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 3


E-MTAB-12040:Sample 4

text: public

text: E-MTAB-12040:Sample 4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 4


E-MTAB-12040:Sample 5

text: public

text: E-MTAB-12040:Sample 5

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 5


E-MTAB-12040:Sample 7

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12040:Sample 7

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 7

characteristic: title


E-MTAB-12040:Sample 8

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12040:Sample 8

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 8


E-MTAB-12040:Sample 21

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12040:Sample 21

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 21


E-MTAB-12040:Sample 22

text: public

text: E-MTAB-12040:Sample 22

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 22


E-MTAB-12040:Sample 23

text: public

text: E-MTAB-12040:Sample 23

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 23


E-MTAB-12040:Sample 24

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12040:Sample 24

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 24

characteristic: title


E-MTAB-12040:Sample 29

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12040:Sample 29

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 29


E-MTAB-12040:Sample 30

characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12040:Sample 30

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 30


E-MTAB-12040:Sample 31

text: public

text: E-MTAB-12040:Sample 31

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: female

text: Sample 31


E-MTAB-12040:Sample 32

text: public

text: E-MTAB-12040:Sample 32

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: Sample 32


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YANGZHOU UNIVERSITY

text: public

tag: Namespace:YANGZHOU UNIVERSITY

characteristic: collection date

text: Salmonella enterica subsp. enterica serovar Kentucky strains isolated from different sources in China

text: China

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Chicken

characteristic: host scientific name

characteristic: isolate

text: Chicken meat

text: Salmonella Kentucky

characteristic: serovar

text: Salmonella enterica subsp. enterica serovar Kentucky strains in China

characteristic: title


characteristic: ENA-CHECKLIST

text: YANGZHOU UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: China

text: not provided

text: Chicken

text: Chicken meat

text: Salmonella enterica subsp. enterica serovar Kentucky

characteristic: organism

text: Salmonella Kentucky


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: YANGZHOU UNIVERSITY

text: public

characteristic: description

text: China

text: not provided

text: Chicken

text: Chicken intestinal contents

text: Salmonella Kentucky


characteristic: External Id

text: YANGZHOU UNIVERSITY

text: public

characteristic: collection date

text: China

characteristic: geographic location (country and/or sea)

text: not provided

text: Chicken

text: Chicken anal swab

text: Salmonella Kentucky


text: YANGZHOU UNIVERSITY

text: public

text: China

text: not provided

characteristic: host health state

text: Environment

characteristic: host scientific name

characteristic: isolate

text: Chicken slaughterhouse Environment

text: Salmonella Kentucky


characteristic: ENA-CHECKLIST

text: YANGZHOU UNIVERSITY

text: public

text: China

text: not provided

text: Human

text: Human

text: Salmonella Kentucky

characteristic: serovar

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:Royal Botanic Gardens, Kew

text: HerbariumKewenseCultivatedPlants

characteristic: collected by

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: RBGKew Living Collection s.n.

characteristic: specimen voucher

text: Thelocactus sp. - RBGKew Living Collection s.n.


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Gonzalez, C.

characteristic: collectorNo

text: spermatophyte root

characteristic: organism

text: spermatophyte root

text: Gonzalez, C. 881 (HTW)

text: Brachyclados megalanthus


characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: Magdalena, C.

text: s.n.

text: spermatophyte root

text: spermatophyte root

text: Magdalena, C. s.n. (K)

text: Victoria sp. - Magdalena, C. s.n. (K)


characteristic: ENA-CHECKLIST

text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: spermatophyte root

text: spermatophyte root

text: Chase, M.W. 313 (K)

text: Acronychia sp. - Chase, M.W. 313 (K)


text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: RBG Kew DNA Bank 2149 (K)

text: Halfordia sp. - RBG Kew DNA Bank 2149 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Klitgaard and Garcia

characteristic: collection date

text: K:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Klitgaard B. 66 (K)

text: Apuleia sp. - Klitgaard B. 66 (K)


text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: LD4 (NBG)

text: Cleretum sp. - LD4 (NBG)

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: HerbariumKewenseCultivatedPlants

text: spermatophyte root

text: spermatophyte root

text: LD31 (K)

text: Machairophyllum sp. - LD31 (K)


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

text: public

text: spermatophyte root

text: spermatophyte root

text: LD46 (NBG)

text: Conicosia sp. - LD46 (NBG)


text: Royal Botanic Gardens, Kew

characteristic: INSDC last update

text: public

text: spermatophyte root

text: spermatophyte root

text: LD48 (NBG)

text: Fenestraria sp. - LD48 (NBG)


text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: LD53 (NBG)

text: Mitrophyllum sp. - LD53 (NBG)


text: Royal Botanic Gardens, Kew

text: public

text: HerbariumKewenseCultivatedPlants

characteristic: collected by

text: spermatophyte root

text: spermatophyte root

text: LD61 (K)

text: Acrodon sp. - LD61 (K)


text: Royal Botanic Gardens, Kew

text: public

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: LD64 (NBG)

text: Carpobrotus sp. - LD64 (NBG)


text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: LD65 (NBG)

characteristic: specimen voucher

text: Chasmatophyllum sp. - LD65 (NBG)


characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: LD72 (NBG)

text: Mesembryanthemum sp. - LD72 (NBG)


characteristic: ENA-LAST-UPDATE

text: Royal Botanic Gardens, Kew

text: public

text: Kennedy, P. B.

text: E:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Kennedy, P. B. 2034 (E)

text: Oryctes sp. - Kennedy, P. B. 2034 (E)


text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

text: Santiago-Valentin, E.

text: WTU:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Santiago-Valentin, E. 96-15 (WTU)

text: Henoonia sp. - Santiago-Valentin, E. 96-15 (WTU)


text: Royal Botanic Gardens, Kew

text: public

characteristic: SRA accession

text: Chungtien, Lijiang & Dali Expedition

text: E:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Anisodus sp. - Chungtien, Lijiang & Dali Expedition 227 (E)


text: Royal Botanic Gardens, Kew

text: public

characteristic: Submitter Id

text: Knapp, S. et al.

text: spermatophyte root

text: spermatophyte root

text: Knapp, S. et al. 10549 (BM)

text: Leptoglossis sp. - Knapp, S. et al. 10549 (BM)


text: Royal Botanic Gardens, Kew

text: public

text: Barboza, G.

characteristic: collectorNo

text: CORD:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Barboza, G. 3704 (CORD)

text: Petunia sp. - Barboza, G. 3704 (CORD)


text: Royal Botanic Gardens, Kew

text: public

text: Särkinen, T. et al

text: spermatophyte root

characteristic: organism

text: spermatophyte root

text: Sarkinen, T. 4833 (BM)

text: Darcyanthus sp. - Sarkinen, T. 4833 (BM)


characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: IEB:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Dodsworth, S. 30 (IEB)

text: Physalis sp. - Dodsworth, S. 30 (IEB)


characteristic: ENA-CHECKLIST

text: Royal Botanic Gardens, Kew

text: public

text: Betancur, J.C. et al.

text: COL:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Betancur, J.C. et al. 15149 (COL)

text: Juanulloa sp. - Betancur, J.C. et al. 15149 (COL)


text: Royal Botanic Gardens, Kew

text: public

text: Knapp, S. et al

text: spermatophyte root

text: spermatophyte root

text: Knapp, S. et al 10516 (BM)

text: Schizanthus sp. - Knapp, S. et al 10516 (BM)


text: Royal Botanic Gardens, Kew

text: public

text: Orejuela, A. et al.

text: spermatophyte root

text: spermatophyte root

text: Orejuela, A. et al. 245 (JBB)

text: Schultesianthus sp. - Orejuela, A. et al. 245 (JBB)


text: Royal Botanic Gardens, Kew

text: public

text: spermatophyte root

text: spermatophyte root

text: Dodsworth, S. 38 (E)

text: Scopolia sp. - Dodsworth, S. 38 (E)


text: Royal Botanic Gardens, Kew

text: public

text: Särkinen, T. et al

text: spermatophyte root

text: spermatophyte root

text: Sarkinen, T. 4020 (BM)

text: Witheringia sp. - Sarkinen, T. 4020 (BM)


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: spermatophyte root

text: spermatophyte root

text: Chase, M.W. 2315 (K)

text: Cyphanthera sp. - Chase, M.W. 2315 (K)


text: Royal Botanic Gardens, Kew

text: public

characteristic: bio material

text: spermatophyte root

text: spermatophyte root

text: Dodsworth, S.68 (NMNL); 944750119

text: Atropanthe sp. - Dodsworth, S.68 (NMNL); 944750119


text: Royal Botanic Gardens, Kew

text: public

text: West

text: s.n

text: BM:Herbarium

text: spermatophyte root

text: spermatophyte root

text: West s.n (BM)

text: Calliphysalis sp. - West s.n (BM)

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: Chiapella et al.

text: CORD:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Chiapella 1455 (CORD)

text: Bouchetia sp. - Chiapella 1455 (CORD)


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

text: public

text: Orejuela, A.

text: spermatophyte root

text: spermatophyte root

text: Orejuela, A. 169 (COL)

text: Markea sp. - Orejuela, A. 169 (COL)


text: Royal Botanic Gardens, Kew

characteristic: INSDC last update

text: public

text: Cardoso, D.

text: BHCB:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Cardoso, D. 1644 (BHCB)

text: Heteranthia sp. - Cardoso, D. 1644 (BHCB)


text: Royal Botanic Gardens, Kew

text: public

text: Carvalho

characteristic: collected by

text: BM:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Carvalho 3672 (BM)

text: Discopodium sp. - Carvalho 3672 (BM)


text: Royal Botanic Gardens, Kew

text: public

text: Ferry, G.

text: s.n.

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: Ferry, G. s.n. (K); NCY013835

text: Rhodospatha sp. - Ferry, G. s.n. (K); NCY013835


text: Royal Botanic Gardens, Kew

text: public

text: Archer, R.H.

text: PRE

text: spermatophyte root

text: spermatophyte root

text: Archer, R.H. 3001 (PRE)

characteristic: specimen voucher

text: Elaeodendron sp. - Archer, R.H. 3001 (PRE)


characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

text: public

text: Archer, R.H.

text: spermatophyte root

text: spermatophyte root

text: Archer, R.H. 2905 (PRE)

text: Erythrostelegia integrifolia


characteristic: ENA-LAST-UPDATE

text: Royal Botanic Gardens, Kew

text: public

text: Archer, R.H.

text: spermatophyte root

text: spermatophyte root

text: Archer, R.H. 2942 (PRE)

text: Hartogiopsis sp. - Archer, R.H. 2942 (PRE)


text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

text: Archer, R.H.

text: spermatophyte root

text: spermatophyte root

text: Archer, R.H. 2997 (PRE)

text: Pseudocatha mandenensis


text: Royal Botanic Gardens, Kew

text: public

characteristic: SRA accession

text: Archer, R.H.

text: spermatophyte root

text: spermatophyte root

text: Archer, R.H. 3004 (PRE)

text: Salvadoropsis sp. - Archer, R.H. 3004 (PRE)


text: Royal Botanic Gardens, Kew

text: public

characteristic: Submitter Id

text: Christenhusz, M.J.M.

characteristic: collection date

text: spermatophyte root

text: spermatophyte root

text: Christenhusz, M.J.M. AU-X-2017 (BC)

text: Calotis sp. - Christenhusz, M.J.M. AU-X-2017 (BC)


text: Royal Botanic Gardens, Kew

text: public

text: Mike Lo

characteristic: collectorNo

text: spermatophyte root

characteristic: organism

text: spermatophyte root

text: Lo, M. AR-4137 (UNIMAS)

text: Hottarum sp. - Lo, M. AR-4137 (UNIMAS)


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: Boufford, D. E.

text: GH:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Boufford, D. E. 43912 (GH)

text: Echinopepon sp. - Boufford, D. E. 43912 (GH)


text: Royal Botanic Gardens, Kew

text: public

text: Forest, F.

text: spermatophyte root

text: spermatophyte root

text: Forest, F. 898 (K)

text: Lagenaria sp. - Forest, F. 898 (K)

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: Takeuchi, W.

text: GH:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Takeuchi, W. 19968 (GH)

text: Papuasicyos sp. - Takeuchi, W. 19968 (GH)


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

text: public

text: Martinez-Calderon, G.

text: GH:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Martinez-Calderon, G. 468 (GH)

text: Polyclathra sp. - Martinez-Calderon, G. 468 (GH)


text: Royal Botanic Gardens, Kew

characteristic: INSDC last update

text: public

text: Cornejo, X.

text: GUAY:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Cornejo, X. 9182 (GUAY)

text: Tecunumania sp. - Cornejo, X. 9182 (GUAY)


text: Royal Botanic Gardens, Kew

text: public

text: Unmounted

characteristic: bio material

text: Vorontsova, M.S.

characteristic: collected by

text: spermatophyte root

text: spermatophyte root

text: Vorontsova, M.S. 1422 (K); Unmounted

text: Sclerodactylon sp. - Vorontsova, M.S. 1422 (K); Unmounted


text: Royal Botanic Gardens, Kew

text: public

text: Johns, R.J.

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: Johns, R.J. 9658 (K)

characteristic: specimen voucher

text: Tapeinochilos sp. - Johns, R.J. 9658 (K)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Royal Botanic Gardens, Kew

text: public

text: Anderson, W.R.

text: spermatophyte root

text: spermatophyte root

text: Anderson, W.R. 13597 (K)

text: Astronium sp. - Anderson, W.R. 13597 (K)


text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Cheek et al.

text: spermatophyte root

text: spermatophyte root

text: Cheek M. 3251 (K)

text: Neobeguea sp. - Cheek M. 3251 (K)


text: Royal Botanic Gardens, Kew

text: public

characteristic: Submitter Id

text: Johns, R.J.

text: spermatophyte root

text: spermatophyte root

text: Johns, R.J. 9795 (K)

text: Semecarpus sp. - Johns, R.J. 9795 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Johns, R.J.

characteristic: collectorNo

text: spermatophyte root

text: spermatophyte root

text: Johns, R.J. 9397 (K)

text: Styphelia sp. - Johns, R.J. 9397 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W. & Fay, M.

characteristic: collection date

text: spermatophyte root

characteristic: organism

text: spermatophyte root

text: Chase, M.W. 14584 (K)

text: Chimaphila sp. - Chase, M.W. 14584 (K)


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Royal Botanic Gardens, Kew

text: public

text: Zarrei, M.

text: spermatophyte root

text: spermatophyte root

text: Zarrei, M. 1332 (K); K001208957

text: Dionysia sp. - Zarrei, M. 1332 (K); K001208957


text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

text: public

text: Kerenga, K.; Cruttwell, N.

text: spermatophyte root

text: spermatophyte root

text: Kerenga, K. s.n. )K); K001393206

text: Sogerianthe sp. - Kerenga, K. s.n. )K); K001393206

characteristic: title


text: Royal Botanic Gardens, Kew

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Forest, F.

text: spermatophyte root

text: spermatophyte root

text: Forest, F. 920 (K)

text: Cadiscus sp. - Forest, F. 920 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Goldblatt, P & Porter, L.

characteristic: collected by

text: spermatophyte root

text: spermatophyte root

text: Goldblatt, P. 12409 (K)

text: Lasiopogon sp. - Goldblatt, P. 12409 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Goldblatt, P & Porter, L.

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: Goldblatt, P. 12577 (K)

text: Garuleum sp. - Goldblatt, P. 12577 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Chase, M.W.

text: spermatophyte root

text: spermatophyte root

text: Chase, M.W. 2183 (K)

characteristic: specimen voucher

text: Spyridium sp. - Chase, M.W. 2183 (K)


characteristic: ENA-FIRST-PUBLIC

text: Royal Botanic Gardens, Kew

text: public

text: Smith, R.J., Hopper, S.D. & Sweedman, L.

text: spermatophyte root

text: spermatophyte root

text: Smith, R.J., 43 (K)

text: Lysiana sp. - Smith, R.J., 43 (K)


characteristic: ENA-LAST-UPDATE

text: YANGZHOU UNIVERSITY

text: public

text: Salmonella enterica subsp. enterica serovar Kentucky strains isolated from different sources in China

characteristic: description

text: China

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Chicken

characteristic: host scientific name

characteristic: isolate

text: Chicken meat

text: Salmonella Kentucky

characteristic: serovar

text: Salmonella enterica subsp. enterica serovar Kentucky strains in China


characteristic: ENA-CHECKLIST

text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: bio material

text: Lewis, M.

characteristic: collection date

characteristic: collectorNo

text: spermatophyte root

characteristic: organism

text: spermatophyte root

text: Lewis, M. 35397 (K); K000370572

text: Dactylaena boliviensis


characteristic: External Id

text: Royal Botanic Gardens, Kew

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Rova et al.

characteristic: collected by

text: GB:Herbarium

characteristic: isolation source

text: spermatophyte root

text: spermatophyte root

text: Rova 2214 (GB)

characteristic: specimen voucher

text: Coccocypselum sp. - Rova 2214 (GB)

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Royal Botanic Gardens, Kew

text: public

text: Persson

text: GB:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Persson 153 (GB)

text: Valantia sp. - Persson 153 (GB)


characteristic: ENA-CHECKLIST

text: Royal Botanic Gardens, Kew

text: public

characteristic: INSDC status

text: Rova et al.

text: GB:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Rova 2535 (GB)

text: Hydnophytum sp. - Rova 2535 (GB)


text: Royal Botanic Gardens, Kew

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Johns, R.J.

text: spermatophyte root

text: spermatophyte root

text: Johns, R.J. 9760 (K)

text: Anthorrhiza sp. - Johns, R.J. 9760 (K)


text: Royal Botanic Gardens, Kew

text: public

text: Davis, A.P.

text: spermatophyte root

text: spermatophyte root

text: Davis, A.P. 3158 (K)

text: Paracephaelis sp. - Davis, A.P. 3158 (K)


text: Royal Botanic Gardens, Kew

text: public

text: O.A. Pérez-Escobar

text: OP 1936

text: K:Herbarium

text: spermatophyte root

text: spermatophyte root

text: Perez-Escobar OP 1936 (K)

text: Acianthera sp. - Perez-Escobar OP 1936 (K)


E-MTAB-11164:Sample 1

text: public

text: E-MTAB-11164:Sample 1

tag: Namespace:Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: narrow-leaved blue lupine

characteristic: common name

text: Protocols: Leaves were sampled at 6, 12, 24, 36, and 48 hours post inoculation. Experiment was performed in controlled environment (a greenhouse), in temperature regime 21 °C day / 19 °C night and under 14 h photoperiod. Seeds were scarified before sowing to brake seed dormancy resulting from hard seed coat and provide even germination. Pots (11 cm × 11 cm × 21 cm) with sterilized soil were used. The inoculation was done using Colletotrichum lupini strain Col-08, obtained in 1999 from the stem of narrow-leafed lupin plants cultivated on field in Wierzenica (52°27′42″N 17°04′05″E) in Great Poland region. The isolate was cultured on SNA medium for 21 days at 20°C under black light to induce sporulation. The inoculation was performed 4 weeks after sowing, when the plants reached 4-6 leaf stage, by spraying of conidial spore suspension in concentration 0,5 x 106 conidia per ml. After inoculation, plants were kept for 24 hours in darkness under ~100% humidity and temperature of 25°C to facilitate conidia germination and infection process. Afterwards, plants were grown under 14-h photoperiod in temperature regime 22°C day / 19°C night and humidity ~70%. Frozen leaf tissue (50 mg) was homogenized in 2 ml tubes (Eppendorf, Hamburg, Germany) and two stainless steel beads (ø 5 mm) using TissueLyser II (Qiagen). SV Total RNA Isolation System (Promega, Madison, WI, USA) was used for RNA isolation without any changes to the protocol except extending DNAse I digestion to 25 min. RNA purity and integrity of the samples prepared for sequencing were measured using an Experion™ Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). TruSeq RNA Sample Preparation v2 Guide, Part # 15026495 Rev. F

characteristic: description

text: seedling development stage

characteristic: developmental stage

characteristic: ecotype

text: wild type genotype

characteristic: genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

characteristic: organism part

text: anthracnose susceptible

characteristic: phenotype

characteristic: replicate

text: Lupinus angustifolius

text: Sample 1


E-MTAB-11164:Sample 10

characteristic: External Id

text: Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11164:Sample 10

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

characteristic: organism

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 10

characteristic: title


E-MTAB-11164:Sample 11

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11164:Sample 11

characteristic: Submitter Id

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 11


E-MTAB-11164:Sample 12

text: public

text: E-MTAB-11164:Sample 12

characteristic: age

text: ArrayExpress

characteristic: broker name

text: narrow-leaved blue lupine

characteristic: common name

characteristic: description

text: seedling development stage

characteristic: developmental stage

characteristic: ecotype

text: wild type genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 12


E-MTAB-11164:Sample 13

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11164:Sample 13

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

characteristic: genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

characteristic: organism part

text: anthracnose susceptible

characteristic: phenotype

characteristic: replicate

text: Lupinus angustifolius

text: Sample 13


E-MTAB-11164:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-11164:Sample 14

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

characteristic: organism

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 14

characteristic: title


E-MTAB-11164:Sample 15

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11164:Sample 15

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 15


E-MTAB-11164:Sample 16

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11164:Sample 16

text: ArrayExpress

text: narrow-leaved blue lupine

characteristic: common name

characteristic: description

text: seedling development stage

characteristic: developmental stage

characteristic: ecotype

text: wild type genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 16


E-MTAB-11164:Sample 17

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11164:Sample 17

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

characteristic: genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

characteristic: organism part

text: anthracnose susceptible

characteristic: phenotype

characteristic: replicate

text: Lupinus angustifolius

text: Sample 17


E-MTAB-11164:Sample 18

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-11164:Sample 18

text: ArrayExpress

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

characteristic: organism

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 18

characteristic: title


E-MTAB-11164:Sample 19

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-11164:Sample 19

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: narrow-leaved blue lupine

text: seedling development stage

text: wild type genotype

text: Lupinus angustifolius

text: Lupinus angustifolius

text: leaf

text: anthracnose susceptible

text: Lupinus angustifolius

text: Sample 19