text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -19.86444, -69.43

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO4


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: TECHNICAL UNIVERSITY MUNICH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:TECHNICAL UNIVERSITY MUNICH

characteristic: Submitter Id

characteristic: collection date

text: leaf sample

characteristic: description

text: Chile

characteristic: geographic location (country and/or sea)

text: -19.86444, -69.43

text: Solanum chilense

characteristic: organism

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO5

characteristic: title


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -19.86444, -69.43

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO6


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -19.86444, -69.43

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO7


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -19.86444, -69.43

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO8


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -19.86444, -69.43

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2751_NO9


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.07028, -70.16306

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2750_N02


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.16917, -70.21222

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2749_NO2


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.24778, -68.36083

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2884_NO5


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.30889, -68.48056

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4329_NO2


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.35083, -68.31972

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4330_N02


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.46806, -70.225

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2932_N02


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.60889, -68.52194

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4332_X1


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -22.9075, -67.94083

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4117A_N05


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -23.1575, -68.035

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4118_N02


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -23.55389, -67.93389

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4119_V16


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -23.63, -68.04444

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4334_NO1


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -23.80361, -68.27528

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4335_NO1


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -23.81667, -68.21667

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA2880_N17


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -24.91417, -70.51611

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4109_NO1


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.0525, -70.47583

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4108_T30


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.26917, -70.43722

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4336_NO1


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.31889, -70.44611

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4107_N01


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.48139, -70.43278

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4106_NO2


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.50222, -70.41139

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4338_NO2


text: TECHNICAL UNIVERSITY MUNICH

text: public

text: leaf sample

text: Chile

text: -25.5375, -70.47222

text: Solanum chilense

text: Solanum chilense

text: mature leaf

text: Solanum chilense - LA4339_NO1


text: University of Helsinki

text: public

tag: Namespace:University of Helsinki

text: Filter with Ag

text: Finland

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: metagenome

text: Treated

characteristic: sewage type

characteristic: surveillance target

text: MK - Ag


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Helsinki

text: public

text: Filter without Ag

text: Finland

text: metagenome

text: metagenome

text: metagenome

text: Treated

text: MK


text: University of Helsinki

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Effluent sewage used as input

text: Finland

text: metagenome

text: metagenome

text: metagenome

text: Effluent

text: WW


text: public

characteristic: SRA accession

tag: Namespace:Max Planck Institute for Plant Breeding Research

characteristic: Submitter Id

text: thale cress

characteristic: common name

characteristic: description

characteristic: ecotype

text: Arabidopsis thaliana

text: Arabidopsis thaliana


text: Max Planck Institute for Plant Breeding Research

text: public

text: thale cress

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

characteristic: title


Hiroshima

text: public

text: Hiroshima

text: thale cress

text: Hiroshima

text: Hiroshima

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Hiroshima


Ishikawa

text: public

text: Ishikawa

text: thale cress

text: Ishikawa

text: Ishikawa

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Ishikawa


Jea

text: public

text: Jea

text: thale cress

text: Jea

text: Jea

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Jea


Shahdara

text: public

text: Shahdara

text: thale cress

text: Shahdara

text: Shahdara

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: Shahdara


text: AZTI

text: public

text: estuarine biome

characteristic: broad-scale environmental context

characteristic: collection date

unit: m

characteristic: depth

text: Station ED10 Winter 2013

characteristic: elevation

text: intertidal sediment

characteristic: environmental medium

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: estuarine biome

characteristic: local environmental context

text: metagenome

text: Functional Profiling

characteristic: project name

text: metagenome

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: AZTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: estuarine biome

text: Station EN17 Winter 2013

text: intertidal sediment

text: Atlantic Ocean

text: estuarine biome

text: metagenome

text: Functional Profiling

text: metagenome

text: metagenome


text: AZTI

text: public

characteristic: Submitter Id

text: estuarine biome

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: depth

text: Station EN20 Winter 2013

characteristic: description

text: intertidal sediment

text: Atlantic Ocean

text: estuarine biome

text: metagenome

characteristic: organism

text: Functional Profiling

text: metagenome

text: metagenome

characteristic: title


text: AZTI

text: public

text: estuarine biome

text: Station EOI15 Winter 2013

characteristic: elevation

text: intertidal sediment

characteristic: environmental medium

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: estuarine biome

characteristic: local environmental context

text: metagenome

text: Functional Profiling

characteristic: project name

text: metagenome

text: metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: AZTI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: estuarine biome

text: Station EOI20 Winter 2013

text: intertidal sediment

text: Atlantic Ocean

text: estuarine biome

text: metagenome

text: Functional Profiling

text: metagenome

text: metagenome


text: AZTI

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: estuarine biome

characteristic: broad-scale environmental context

characteristic: collection date

characteristic: depth

text: Station EOK10 Winter 2013

characteristic: description

text: intertidal sediment

text: Atlantic Ocean

text: estuarine biome

text: metagenome

text: Functional Profiling

text: metagenome

text: metagenome


text: AZTI

text: public

text: estuarine biome

text: Station EU08 Winter 2013

characteristic: elevation

text: intertidal sediment

characteristic: environmental medium

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: estuarine biome

text: metagenome

characteristic: organism

text: Functional Profiling

text: metagenome

text: metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: AZTI

characteristic: INSDC center name

text: public

text: marine benthic biome

text: Station LOK10 Winter 2013

text: shallow marine sediment

text: Atlantic Ocean

text: marine benthic biome

characteristic: local environmental context

text: metagenome

text: Functional Profiling

characteristic: project name

text: metagenome

text: metagenome


text: University of Glasgow

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Glasgow

characteristic: Submitter Id

characteristic: collection date

text: African malaria mosquito

characteristic: common name

text: An. gambiae whole mosquito

text: Burkina Faso

text: Anopheles gambiae

text: Anopheles gambiae


text: Ifremer

text: public

text: 5'-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA-3';5'-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3'

characteristic: adapters

text: SeBiMER

characteristic: broker name

text: Ifremer

characteristic: collecting institution

text: Pacific pearl-oyster

text: No

text: French Polynesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Centre Ifremer du Pacifique, Tahiti, Polynesie francaise

characteristic: geographic location (region and locality)

text: eukaryote

characteristic: investigation type

text: whole individual

text: Pinctada margaritifera

text: D-stage

text: Pinctada margaritifera

text: Sequencing by synthesis (Illumina)

characteristic: sequencing method

text: D-stage larva


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ifremer

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SeBiMER

text: Ifremer

text: Pacific pearl-oyster

text: No

text: French Polynesia

text: eukaryote

text: whole individual

text: Pinctada margaritifera

characteristic: organism

characteristic: project name

text: Velyger

text: Pinctada margaritifera

text: Sequencing by synthesis (Illumina)

text: Velyger larva

characteristic: title


text: Ifremer

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

text: SeBiMER

characteristic: broker name

text: Ifremer

characteristic: collecting institution

characteristic: collection date

text: Pacific pearl-oyster

characteristic: common name

text: No

text: French Polynesia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: eukaryote

text: whole individual

text: Pinctada margaritifera

text: Umbo

text: Pinctada margaritifera

text: Sequencing by synthesis (Illumina)

text: Umbo larva


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ifremer

text: public

text: SeBiMER

text: Ifremer

text: Pacific pearl-oyster

text: No

text: French Polynesia

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: geographic location (region and locality)

text: eukaryote

characteristic: investigation type

text: whole individual

text: Pinctada margaritifera

text: Eye-stage

text: Pinctada margaritifera

text: Sequencing by synthesis (Illumina)

characteristic: sequencing method

text: Eye-stage larva


text: University Lyon 1 Claude Bernard

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21687

tag: Namespace:University Lyon 1 Claude Bernard

characteristic: Submitter Id

characteristic: description

text: Legionella pneumophila

characteristic: organism

text: Legionella pneumophila

characteristic: serotype

text: Paris

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21688

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21689

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21690

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21691

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21692

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21693

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-15-05-2023-09:33:09:471-21695

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-16-05-2023-09:12:38:614-22108

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: University Lyon 1 Claude Bernard

text: public

text: ena-SAMPLE-TAB-16-05-2023-09:12:38:614-22109

text: Legionella pneumophila

text: Legionella pneumophila

text: Paris


text: Plasmodium falciparum

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

text: Plasmodium falciparum


text: UNIVERSITY OF OULU

text: public

tag: Namespace:UNIVERSITY OF OULU

characteristic: broad-scale environmental context

characteristic: collection date

text: human

characteristic: environmental medium

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: local environmental context

text: Homo sapiens

text: RNA-seq of GATA2 and SMAD4 in prostate 1F5 cells

characteristic: project name

text: Homo sapiens


text: UNIVERSITY OF OULU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: description

text: Finland

text: Homo sapiens

characteristic: organism

text: ChIP-seq of GATA2 and SMAD4 in prostate 1F5 and LNCaP cells

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF OULU

text: public

text: LNCaP

text: human

characteristic: common name

text: LNCaP

text: Finland

text: LNCaP

text: Homo sapiens

text: Homo sapiens

characteristic: title


name: SAMIN0003236-Pre-plantation Yamuna floodplain soil amended with cow dung manure

text: public

tag: Namespace:Sophayo Mahongnao, Daulat Ram College, University of Delhi

text: IBDC

characteristic: broker name

text: Department of Biochemistry, Daulat Ram College, University of Delhi

text: The Yamuna floodplain soil was amended with cow dung manure in the ratio of 5 parts of soil with 1 part of cow dung manure. The soil was collected from the Yamuna river bank during the month of March-April.

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: DELHI National Capital Region

characteristic: geographic location (region and locality)

text: soil metagenome

text: soil metagenome


name: SAMIN0003237-Pre-plantation soil of Yamuna floodplain amended with leaf waste compost

text: Sophayo Mahongnao, Daulat Ram College, University of Delhi

characteristic: INSDC center name

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with leaf waste compost in the ratio of 5 parts of soil with 1 part of compost. The soil sample was collected from the Yamuna river bank during Spring season. The soil was collected from the Yamuna river bank during the month of March-April.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003238-Pre-plantation soil of Yamuna floodplain amended with kitchen waste compost

characteristic: INSDC first public

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with kitchen waste compost in the ratio of 5 parts of soil with 1 part of compost. The soil sample was collected from the Yamuna river bank during Spring season. The soil was collected from the Yamuna river bank during the month of March-April.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003239-Pre-plantation soil amended with municipal organic waste compost

characteristic: INSDC last update

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with municipal organic waste compost in the ratio of 5 parts of soil with 1 part of compost. The soil sample was collected from the Yamuna river bank during Spring season. The soil was collected from the Yamuna river bank during the month of March-April.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003240-Pre-plantation soil of Yamuna river bank amended with vermicompost

text: public

characteristic: INSDC status

text: IBDC

text: The Yamuna floodplain soil was amended with vermicompost in the ratio of 5 parts of soil with 1 part of compost. The soil sample was collected from the Yamuna river bank during Spring season, in the month of March-April.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003241-Pre-plantation soil of Yamuna floodplain amended with chemical fertilizer

text: public

characteristic: SRA accession

text: IBDC

text: The Yamuna floodplain soil was amended with chemical fertilizer, DAP. The soil sample was collected from the Yamuna river bank during Spring season, in the month of March-April.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003242-Post-harvest soil of Yamuna floodplain amended with cow dung manure planted with red amaranth

text: public

characteristic: Submitter Id

text: IBDC

text: The Yamuna floodplain soil was amended with cow dung manure and planted with red amaranth in experimental pot. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003243-Post-harvest soil of Yamuna floodplain amended with leaf waste compost, planted with red amaranth

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with leaf waste compost and planted with red amaranth in experimental pots. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

characteristic: description

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003244-Post-harvest soil of Yamuna floodplain amended with kitchen waste compost, planted with red amaranth

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with kitchen waste compost and planted with red amaranth in experimental pot. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

characteristic: organism

text: soil metagenome


name: SAMIN0003246-Post-harvest soil of Yamuna floodplain amended with vermicompost. planted with red amaranth

characteristic: ENA-CHECKLIST

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with vermicompost and planted with red amaranth in experimental pots. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003245-Post-harvest soil of Yamuna floodplain amended with municipal organic waste compost, planted with red amaranth

characteristic: ENA-FIRST-PUBLIC

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with municipal organic waste compost and planted with red amaranth in experimental pot. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


name: SAMIN0003247-Post-harvest soil of Yamuna floodplain amended with chemical fertilizer, planted with red amaranth

characteristic: ENA-LAST-UPDATE

text: public

text: IBDC

text: The Yamuna floodplain soil was amended with chemical fertilizer and planted with red amaranth in experimental pot. The plantation was done in the month of Mars-April and harvested in June. The soil sample was collected after harvest.

text: Yes

text: India

text: DELHI National Capital Region

text: soil metagenome

text: soil metagenome


characteristic: External Id

text: Thuenen-Institute of Fisheries Ecology

text: public

tag: Namespace:Thuenen-Institute of Fisheries Ecology

characteristic: collection date

text: Atlantic cod

text: Baltic cod, historical

text: Baltic Sea

text: SD 25

text: Gadus morhua

text: Gadus morhua

text: M

characteristic: sex


text: Thuenen-Institute of Fisheries Ecology

text: public

text: Atlantic cod

characteristic: common name

text: Baltic cod, historical

text: Baltic Sea

text: SD 25

text: Gadus morhua

text: Gadus morhua

text: F

characteristic: title


text: Thuenen-Institute of Fisheries Ecology

text: public

text: Atlantic cod

text: Baltic cod, historical

text: Baltic Sea

characteristic: geographic location (country and/or sea)

text: SD 22

characteristic: geographic location (region and locality)

text: Gadus morhua

text: Gadus morhua

text: M


text: Vaiomer

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

text: Feces

characteristic: tissue


characteristic: ENA first public

text: UNIVERSITY HOHENHEIM

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY HOHENHEIM

text: Control

text: mouse gut metagenome

text: mouse gut metagenome

text: mouse samples


characteristic: ENA-CHECKLIST

text: UNIVERSITY HOHENHEIM

text: public

characteristic: Submitter Id

text: FFr

characteristic: description

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: mouse samples


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: INSERM U955

text: public

tag: Namespace:INSERM U955

characteristic: collection date

text: human

text: France

text: Homo sapiens

text: Homo sapiens

text: HCC


text: Thuenen-Institute of Fisheries Ecology

text: public

text: Atlantic cod

characteristic: common name

text: Celtic Sea cod, modern

text: Atlantic Ocean

characteristic: geographic location (country and/or sea)

text: Celtic Sea

text: 50.996, -5.313

text: Gadus morhua

text: Gadus morhua

text: M

characteristic: sex

characteristic: title


text: Thuenen-Institute of Fisheries Ecology

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Atlantic cod

text: Celtic Sea cod, modern

text: Atlantic Ocean

text: Celtic Sea

characteristic: geographic location (region and locality)

text: 50.911, -5.309

text: Gadus morhua

text: Gadus morhua

text: F


text: Thuenen-Institute of Fisheries Ecology

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Atlantic cod

text: Celtic Sea cod, modern

text: Atlantic Ocean

text: Celtic Sea

text: 51.033, -5.280

text: Gadus morhua

text: Gadus morhua

text: M


characteristic: ENA-CHECKLIST

text: Thuenen-Institute of Fisheries Ecology

text: public

characteristic: SRA accession

text: Atlantic cod

text: Celtic Sea cod, modern

text: Atlantic Ocean

text: Celtic Sea

text: 51.033, -5.280

text: Gadus morhua

text: Gadus morhua

text: F


text: Thuenen-Institute of Fisheries Ecology

text: public

characteristic: Submitter Id

text: Atlantic cod

text: Baltic cod, modern

characteristic: description

text: Baltic Sea

text: SD 26

text: 55.2135, 18.5173333333

text: Gadus morhua

text: Gadus morhua


characteristic: ENA-FIRST-PUBLIC

text: IIMCB

text: public

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Animals were euthanized and bladders were excised and kept on ice in Hypothermosol solution. Bladders were removed, and minced with sterile scissors and 2ml of Digestion solution was added (Ca/Mg-free PBS, 0.5mM EDTA pH8, 10mg/ml of Bacillus Licheniformis psychrophilic protease). Samples were incubated on ice for 20 min. Every minute they were flicked to mix, and every 2 min they were triturated using 1000 μl pipette with a cut tip. Then samples were split to three 1.7ml tubes and further incubated to 8 minutes, while homogenized with plastic pestle 10 strokes, every 2 min. Then samples were mixed thoroughly and centrifuged for 30s at 500g at 4 °C and sample was divided to 70% of top supernatant fraction, which was filtered trough 100-μm mesh, 5ml of Ca/Mg-free PBS was added and set aside on ice. The pellet was digested again. 1ml of Digestion solution was added and every minute they were flicked to mix, and every 2 min they were triturated using 1000 μl pipette with a cut tip. Then, the sample was filtered through 100-μm mesh, 5ml of Ca/Mg-free PBS was added and it was combined with first fraction. Cells were collected by centrifugation for 7 min at 500g at 4 °C. Then the pellet was resuspended in 300 μl of ACK buffer, incubated at room temperature for 1 min. Subsequently, 13 ml of cold Ca/Mg-free PBS was added, and samples were centrifuged at 500g 7 min at 4 °C. The cells were then incubated for one hour on ice in 100 μl Miltenyi Dead Cell Removal kit beads, after which 3 ml of kit Binding Buffer was added to each sample. The samples were then loaded onto LS-columns and the flow-through was collected. To increase cell recovery, columns were washed 3 times with 12ml of Binding Buffer. The flow through was then centrifuged 7 min 500g and was resuspended in Ca/Mg-free PBS with 0.04% BSA and samples proceeded directly to scRNAseq. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: germ free

characteristic: growth condition

characteristic: individual

text: Mus musculus

characteristic: organism

text: Mus musculus

text: urinary bladder

characteristic: organism part

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: adult

text: wild type genotype

text: specific pathogen free

text: Mus musculus

text: Mus musculus

text: urinary bladder

text: Mus musculus

text: male

characteristic: sex

characteristic: title


E-MTAB-12999:Sample 10

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Center of Functional Genomics, Berlin Institute of Health at Charite - Universitatsmedizin Berlin

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12999:Sample 10

tag: Namespace:Center of Functional Genomics, Berlin Institute of Health at Charite – Universitatsmedizin Berlin

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Protocols: For RNA extraction from whole adrenal cortices, extracted adrenal glands from 6 WT and 6 KO (3 male, 3 females each) were rapidly transferred into PBS on ice. After the removal of the surrounding fat, the glands were cut in half, manually separated from the medulla and placed in RNAlater (ThermoFisher). Total RNA was isolated using the RNeasy Mini Kit (Qiagen) with subsequent DNAse digestion according to the manufacturer’s instructions. Purified RNA was then further processed at the Core Unit Genomics of the Berlin Institute of Health at Charité - Universitätsmedizin Berlin. Ribosomal RNA was depleted and cDNA transcribed using the TruSeq Stranded Total RNA kit (Illumina).

characteristic: description

text: Cacna1h -/-

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

text: Sample 10


E-MTAB-12999:Sample 11

text: public

text: E-MTAB-12999:Sample 11

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Cacna1h -/-

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: female

text: Sample 11


E-MTAB-12999:Sample 12

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12999:Sample 12

text: ArrayExpress

text: house mouse

text: Cacna1h -/-

text: Mus musculus

text: Mus musculus

text: adrenal cortex

characteristic: organism part

text: Mus musculus

text: female

characteristic: strain

text: Sample 12


E-MTAB-12999:Sample 7

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12999:Sample 7

text: ArrayExpress

text: house mouse

characteristic: common name

text: Cacna1h -/-

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

characteristic: sex

text: Sample 7


E-MTAB-12999:Sample 8

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: E-MTAB-12999:Sample 8

text: ArrayExpress

text: house mouse

text: Cacna1h -/-

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

text: Sample 8

characteristic: title


E-MTAB-12999:Sample 9

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12999:Sample 9

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: Cacna1h -/-

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: female

text: Sample 9


E-MTAB-12999:Sample 1

text: public

text: E-MTAB-12999:Sample 1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: female

text: Sample 1


E-MTAB-12999:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-12999:Sample 2

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: adrenal cortex

characteristic: organism part

text: Mus musculus

text: female

characteristic: strain

text: Sample 2


E-MTAB-12999:Sample 3

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-12999:Sample 3

text: ArrayExpress

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

characteristic: sex

text: Sample 3


E-MTAB-12999:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: E-MTAB-12999:Sample 4

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: female

text: Sample 4

characteristic: title


E-MTAB-12999:Sample 5

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12999:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

text: Sample 5


E-MTAB-12999:Sample 6

text: public

text: E-MTAB-12999:Sample 6

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: wild type genotype

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: adrenal cortex

text: Mus musculus

text: male

text: Sample 6


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WIS

text: public

text: ArrayExpress

text: mix

text: house mouse

text: Protocols: Mice were sacrificed and their back was shaved using a trimmer. Hair removal cream (Veet) was used to remove all the remaining hairs. Back skin was taken and preserved in Hypothermosol (H4416, Sigma), on ice. Later, the tissue was cut to two pieces, one was used to isolate immune cells and the other was used to isolate non-immune cells. For isolating the immune cells, the skin piece was cut to small pieces and then digested using 2 mg/ml Collagenase II (C6885, Sigma), 0.5 mg/ml Hyaluronidase (H3506, Sigma), and 0.1 mg/ml DNase I (DN25, Sigma) in IMDM medium at 37°C for 40 min. Then, the sample was passed through 70-µm cell strainer and rinsed three times with cold Ca/Mg-free HBSS. The remaining undigested tissue (remained in the cell strainer) was treated in 0.05% trypsin-EDTA for 15 min at 37°C. Then, the sample was passed through a 70 µm cell strainer and rinsed three times with cold Ca/Mg-free HBSS and combined with the first fraction. Then the cells were centrifugated at 500g for 10 min. The pellet was resuspended in 500 μl Miltenyi Dead Cell Removal kit beads, after which 5.5 ml of kit Binding Buffer was added to each sample. The samples were filtered and then loaded onto LS-columns and the flow-through was collected and centrifuged 10 min 500g. We resuspended the pellet in 100 μl of Ca/Mg-free PBS with 1% FCS and incubated for 5 min with 1μg/ml anti-CD16/32 (Biolegend) to block Fc receptors before adding the 1:500 CD45.2 FITC antibody (104, Biolegend). The cells were incubated for 1h on ice, then 1:10.000 dilution of DAPI was added and stained for additional 3 min. Then 10 ml of Ca/Mg-free PBS was added, and the cells were centrifuged for 10 min at 500g. The supernatant was removed, and the cells were resuspended in PBS, filtered through a 40-μm mesh and DAPI negative and CD45 positive cells were sorted on BD FACSAria III Fusion. Sorted cells were then centrifuged 10min at 500g, resuspended in Ca/Mg-free PBS with 0.04% BSA and counted. For isolating the non-immune fraction, the tissue was cut to small pieces and then Digestion solution was added (Ca/Mg-free PBS, 0.5mM EDTA pH8, 10mg/ml of Bacillus Licheniformis psychrophilic protease) and incubated on ice for 20 min and triturated using 1000 μl pipette with a cut tip every two minutes. Then, digested tissue was further homogenized using 2 mL mortar and pestle homogenizer. To remove undigested pieces of tissue, the samples were centrifugated at 500g for 30 seconds. The supernatant was filtered through 40-μm cell strainer and centrifugated at 500g for 10 min. The pellet was resuspended in 500 μl Miltenyi Dead Cell Removal kit beads, after which 5.5 ml of kit Binding Buffer was added to each sample. The samples were filtered and then loaded onto LS-columns and the flow-through was collected and centrifuged 10 min 500g. We resuspended the pellet in 100 μl of Ca/Mg-free PBS with 1% FCS and incubated for 5 min with 1μg/ml anti-CD16/32 (Biolegend) to block Fc receptors before adding the 1:500 CD45.2 FITC antibody (104, Biolegend). The cells were incubated for 1h on ice, then 1:10.000 dilution of DAPI was added and stained for additional 3 min. Then 10 ml of Ca/Mg-free PBS was added, and the cells were centrifuged for 10 min at 500g. The supernatant was removed, and the cells were resuspended in PBS, filtered through a 40-μm mesh and DAPI negative and CD45 negative cells were sorted on BD FACSAria III Fusion. Sorted cells were then centrifuged 10min at 500g, resuspended in Ca/Mg-free PBS with 0.04% BSA and counted. Before loading onto 10x Genomics Chromium immune and non-immune cells were mixed at 1:1 ratio. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

text: adult

characteristic: developmental stage

text: wild type genotype

text: germ free

characteristic: growth condition

characteristic: individual

text: Mus musculus

text: Mus musculus

text: skin of body

characteristic: organism part

text: Mus musculus

text: male

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: WIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: mix

text: house mouse

characteristic: common name

text: adult

text: wild type genotype

text: specific pathogen free

text: Mus musculus

text: Mus musculus

text: skin of body

text: Mus musculus

text: male

characteristic: sex


name: SAMIN0003308-Underground water of DRC college campus

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: IBDC

characteristic: broker name

text: Department of Biochemistry, Daulat Ram College, University of Delhi

text: The sample was collected from the Daulat Ram College Campus, university of Delhi, North campus. It is a freshly pump-out underground water collected in a sterilized bottle and analysed through 16S metgenomics

characteristic: description

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: DELHI

characteristic: geographic location (region and locality)

text: groundwater metagenome

text: groundwater metagenome

text: Underground water of DRC college campus

characteristic: title


name: SAMIN0003309-16S metagenomic profiling of the underground water of Burari area, North Delhi

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sophayo Mahongnao, Daulat Ram College, University of Delhi

text: public

text: IBDC

text: 16S metagenomic profiling of the underground water collected from Yamuna floodplain at the Burari area, north Delhi, was performed to analysed the bacteria present in the samples.

text: Yes

text: India

text: Burari, North Delhi

text: groundwater metagenome

characteristic: organism

text: groundwater metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IIMCB

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Epididymal-adipose tissue from mice was dissected and placed in 5 ml of DMEM (without phenol red, 4.5 g/l glucose) at room temperature and disintegrated by chopping with sterile scissors. Subsequently, 0.2 g/ml of Collagenase II was added, and samples were incubated for 20 min at 37 °C while shaking. Subsequently, 5 ml of cold DMEM was added to each sample and filtered through a 250-μm mesh. Samples were centrifuged at room temperature for 5 min at 300g without breaks and with slow acceleration. The pellets containing immune cells as well as top layer containing adipocytes were recovered using glass Pasteur pipettes. Immune cell fraction was resuspended in 0.5 ml ACK buffer (Gibco, A1049201), and incubated for 1 min at room temperature. Then, 14 ml of PBS was added, and cells were collected by centrifugation at 500g for 10 min. Pellets were resuspended in Ca/Mg-free PBS with 0.04% BSA, filtered through a 40-µm mesh. To adipocyte fraction was three times the volume (i.e. ~3 ml) of ice-cold NST Lysis Buffer (0.1% NP40, 10 mM Tris-HCl, 146 mM NaCl, 1 mM CaCl2, 21 mM MgCl2, 40 U/ml RNase Inhibitor)23 was added and incubated on ice for 5 min to isolate nuclei, then sample was centrifugated for 5 min at 500g at 4 °C and resuspended in 1ml of Wash Buffer (Ca/Mg-free PBS, 1% BSA, 0.2U/μl RNase Inhibitor). Wash was repeated, nuclei were filtered through 65-μm mesh and counted using Trypan blue. Fractions were combined to obtain 50% cell fraction and 50% nuclei fraction before loading onto 10x Genomics Chromium. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: germ free

characteristic: growth condition

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epididymal fat pad

characteristic: organism part

text: Mus musculus

text: female

characteristic: strain


text: IIMCB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

text: adult

text: wild type genotype

text: germ free

text: Mus musculus

text: Mus musculus

text: epididymal fat pad

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

text: public

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: wild type genotype

text: specific pathogen free

text: Mus musculus

characteristic: organism

text: Mus musculus

text: epididymal fat pad

text: Mus musculus

text: female

characteristic: title


text: IIMCB

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: specific pathogen free

characteristic: growth condition

characteristic: individual

text: Mus musculus

text: Mus musculus

text: epididymal fat pad

characteristic: organism part

text: Mus musculus

text: male

characteristic: strain


name: SAMIN0003310-Groundwater of DRC campus for ITS analysis

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: IBDC

characteristic: broker name

text: This ground water was collected from the Daulat Ram College campus, North Delhi for ITS metagenomic analysis

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: DELHI

characteristic: geographic location (region and locality)

text: groundwater metagenome

text: groundwater metagenome


name: SAMIN0003311-Groundwater of Yamuna river bank, Burari area, for ITS analysis

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: IBDC

characteristic: common name

text: The groundwater samples was collected from the Yamuna river bank at Burari area, North Delhi, for ITS analysis

characteristic: description

text: Yes

text: India

text: DELHI

text: groundwater metagenome

characteristic: organism

text: groundwater metagenome

characteristic: title


text: IIMCB

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

text: house mouse

text: Protocols: Animals were sacrificed using injection of pentobarbital and the lung was perfused with cold PBS. Subsequently a catheter was inserted into the trachea and 1 ml of 5 mg/ml Dispase solution was injected. The solution was incubated for 5 min in the lungs before it was excised and placed in IMDM on ice. The lung was then minced and incubated with an enzyme mix containing 1 mg/ml Dnase I, 2 mg/ml Collagenase IV and 5mg/ml Dispase for 20 min at 37 °C, shaking. The lung was then transferred to a 70 μm cell strainer and smashed through with 20 ml Ca/Mg-free PBS to get a single cell suspension. The cells were then collected at 4 °C for 10 min at 500g. The pellets were resuspended in 1ml ACK buffer (Gibco, A1049201) and incubated for 1 min at room temperature. Then 14 ml of Ca/Mg-free PBS was added, and cells were centrifuged at 500g for 7 min. The cells were then incubated for one hour on ice in 500 μl Miltenyi Dead Cell Removal kit beads, after which 5.5 ml of kit Binding Buffer was added to each sample. The samples were filtered and then loaded onto LS-columns and the flow-through was collected. The flow through was then centrifuged 7 min 500g and was resuspended in Ca/Mg-free PBS with 0.04% BSA and samples proceeded directly to scRNAseq. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: germ free

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: lung

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IIMCB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: adult

text: wild type genotype

text: specific pathogen free

text: not applicable

text: Mus musculus

text: Mus musculus

text: lung

text: Mus musculus

text: female


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Small intestine epithelium. Whole small intestine was dissected from the animal, and tissue was cut longitudinally to remove contents and vortexed in clean 4 °C Ca/Mg-free PBS to wash it. This was repeated until solution was clear. 20 ml of 4 °C Dissociation Buffer (Ca/Mg-free HBSS, 2.5 mM EDTA pH 8) was added and incubated shaking at 4 °C for 40 min to dissociate epithelial layer. Tissue was removed and epithelium was collected by centrifugation at 500g for 3 min. To obtain single cell solution from crypts we resuspended the pellet in 10 ml of prewarmed 0.25% Trypsin-EDTA solution and incubated for 20 min at 37 °C while shaking. Then we added 20 ml of cold Ca/Mg-free PBS, and the samples were then filtered using 65-μm mesh. Finally, cells were collected at 500g 4 °C for 5 min and resuspended in cold Ca/Mg-free PBS with 0.04% BSA. Small intestine lamina propria. Whole small intestine was dissected from the animal, Payers patched were dissected and removed and tissue was cut longitudinally to remove contents. Then it vortexed in clean 4 °C Ca/Mg-free PBS to wash it. This was repeated until solution was clear. 12 ml of 37 °C Dissociation Buffer (Ca/Mg-free HBSS, 5 mM EDTA pH 8) was added and incubated shaking at 37 °C for 5 min to dissociate epithelial layer. Then tissue was vortexed epithelial layer stripping and moved to fresh 10 ml of Dissociation Buffer and incubated shaking at 37 °C for 15 min. Then, the tissue was placed in cold Ca/Mg-free HBSS, washed three times using vortex and dried on clean paper. To disintegrate colon tissue was first chopped with scissors and subsequently incubated shaking in Digestion Buffer (RPMI, 10% FCS, 0.625 mg/ml collagenase D, 1 mg/ml dispase and 0.04 mg/ml liberase TM) at 37 °C for 35 min. 10ml of cold Ca/Mg-free HBSS was then added to stop digestion and cells were passed through 85μm metal mesh. Then cells were collected by centrifugation at 500g for 8 min at 4 °C. To lyse erythrocytes pellets were resuspended in 1 ml ACK buffer and incubated for 1 min at room temperature. Then 10ml of Ca/Mg-free PBS was added, cells were centrifuged at 500g for 8 min. To remove dead cells and to ensure depletion of epithelium we resuspended the pellet in 100 μl of Ca/Mg-free PBS with 1% FCS and incubated for 5 min with 1 μgl/ml anti-CD16/32 (Biolegend) to block Fc receptors before adding the 1:100 EPCAM APC-Cy7 antibody (G8.8, Biolegend). The cells were incubated for 30 min on ice, then 1:10.000 dilution of DAPI was added and stained for additional 3 min. Then 10 ml of Ca/Mg-free PBS was added, and the cells were centrifuged for 8 min at 500g. The supernatant was removed,and the cells were resuspended in Ca/Mg-free PBS, filtered through a 40μm mesh and DAPI negative and EPCAM negative cells were sorted on BD FACSAria III. Sorted cells were then centrifuged 8 min at 500g, resuspended in Ca/Mg-free PBS with 0.04% BSA and counted. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

characteristic: description

text: adult

text: wild type genotype

text: germ free

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine epithelium

text: Mus musculus

text: male

characteristic: title


text: IIMCB

text: public

text: ArrayExpress

text: house mouse

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: specific pathogen free

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: small intestine epithelium

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IIMCB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: adult

text: wild type genotype

text: germ free

text: not applicable

text: Mus musculus

text: Mus musculus

text: small intestine lamina propria

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

text: specific pathogen free

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: small intestine lamina propria

text: Mus musculus

text: male

characteristic: title


text: IIMCB

text: public

text: ArrayExpress

text: house mouse

text: Protocols: Colon epithelium. Whole colon was dissected from the animal, and tissue was cut longitudinally to remove contents and vortexed in clean 4 °C Ca/Mg-free PBS to wash it. This was repeated until solution was clear. 25 ml of 37 °C Dissociation Buffer (Ca/Mg-free HBSS, 2 mM EDTA pH 8, 1 mM DTT) was added and incubated shaking at 37 °C for 30 min to dissociate epithelial layer. Tissue was removed and epithelium was collected by centrifugation at 500g for 3 min. The cells were then incubated for one hour on ice in 500 μl Miltenyi Dead Cell Removal kit beads, after which 5.5 ml of kit Binding Buffer was added to each sample. The samples were filtered and then loaded onto LS-columns and the flow-through was collected. The flow-through was then centrifuged 5 min 500g and was resuspended in Ca/Mg-free PBS with 0.04% BSA and samples proceeded directly to scRNAseq. Colon lamina propria. Whole colon was dissected from the animal and cut longitudinally to remove contents and tissue was vortexed in clean 4 °C Ca/Mg-free PBS to wash it. This was repeated until solution was clear. 10 ml of 37 °C Dissociation Buffer (Ca/Mg-free HBSS, 3 mM EDTA pH 8, 1 mM DTT) was added and incubated shaking at 37 °C for 15 min to dissociate epithelial layer. Then tissue was vortexed epithelial layer stripping and moved to fresh 10ml of Dissociation Buffer and incubated shaking at 37 °C for 20 min. Then, the tissue was placed in cold Ca/Mg-free HBSS, washed twice using vortex and dried on clean paper. To disintegrate colon tissue was first chopped with scissors and subsequently incubated shaking in Digestion Buffer (RPMI, 10% FCS, 0.8 mg/ml collagenase D, 1.6 mg/ml dispase) at 37 °C for 35 min. 10 ml of cold Ca/Mg-free HBSS was then added to stop digestion and cells were passed through 85-μm metal mesh. Then cells were collected by centrifugation at 500g for 8 min at 4 °C. To lyse erythrocytes pellets were resuspended in 1 ml ACK buffer and incubated for 1 min at room temperature. Then 10 ml of Ca/Mg-free PBS was added, cells were centrifuged at 500g for 8 min. To remove dead cells and to ensure depletion of epithelium we resuspended the pellet in 100 μl of Ca/Mg-free PBS with 1% FCS and incubated for 5 min with 1μg/ml anti-CD16/32 (Biolegend) to block Fc receptors before adding the 1:100 EPCAM APC-Cy7 antibody (G8.8, Biolegend). The cells were incubated for 30 min on ice, then 1:10.000 dilution of DAPI was added and stained for additional 3 min. Then 10 ml of Ca/Mg-free PBS was added, and the cells were centrifuged for 8 min at 500g. The supernatant was removed,and the cells were resuspended in PBS, filtered through a 40-μm mesh and DAPI negative and EPCAM negative cells were sorted on BD FACSAria III. Sorted cells were then centrifuged 8 min at 500g, resuspended in Ca/Mg-free PBS with 0.04% BSA and counted. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: germ free

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: colon epithelium

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IIMCB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: adult

text: wild type genotype

text: specific pathogen free

text: not applicable

text: Mus musculus

text: Mus musculus

text: colon epithelium

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

text: germ free

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: colon lamina propria

text: Mus musculus

text: male

characteristic: title


text: IIMCB

text: public

text: ArrayExpress

text: house mouse

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: specific pathogen free

characteristic: growth condition

characteristic: individual

text: not applicable

characteristic: isolate

text: Mus musculus

text: Mus musculus

text: colon lamina propria

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: IIMCB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Liver cells were isolated using a modified protocol of Mederacke et al.22 In brief, using a peristaltic pump we performed retrograde liver perfusion into the inferior vena cava with three solutions: (1) EGTA (8 g/l NaCl, 0.4 g/l KCl, 88 mg/l NaH2PO4∙H2O, 120 mg/l Na2HPO4∙H2O, 2.38 g/l HEPES, 0.35 g/l NaHCO3, 0.19 g/l EGTA, 0.9 g/l glucose) for 2 min; (2) pronase (0.4 mg/ml Protease from Streptomyces griseus in EBS buffer: 8 g/l NaCl, 0.4 g/l KCl, 88 mg/l NaH2PO4∙H2O, 120 mg/l Na2HPO4∙H2O, 2.38 g/l HEPES, 0.35 g/l NaHCO3, 0.42 g/l CaCl2) for 5 min; and (3) collagenase D (0.1U/ml collagenase D in EBS buffer) for 7 min. The liver was then dissected, placed in cold EBS solution and shaken vigorously with forceps to allow separation of single cells. The solution was filtered through 100-μm mesh and hepatocytes were depleted by centrifugation at 30g for 5 min. Cells were then collected by centrifugation at 580g and resuspended in cold Ca/Mg-free PBS. To enrich for stellate cells, we sorted cells with retinoid fluorescence in the channel excitation 405, emission 450/40 using a BD FACSAria III. We then mixed stellate and unsorted cells in 1:1 ratio, spun them down, resuspended them in Ca/Mg-free PBS with 0.04% BSA and counted them using a Neubauer chamber, before proceeding to single-cell RNA-seq. according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v2 User Guide according to 10x genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v2 User Guide

text: adult

text: wild type genotype

text: germ free

text: not applicable

text: Mus musculus

text: Mus musculus

text: liver

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IIMCB

characteristic: INSDC center name

text: public

characteristic: age

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: adult

text: wild type genotype

text: specific pathogen free

text: not applicable

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: Mus musculus

text: male

characteristic: title


name: SAMIN0003312-Red Amaranth grown with Fertilizer in Yamuna soil

text: public

tag: Namespace:Pooja Sharma, Daulat Ram College, University of Delhi

text: IBDC

characteristic: collection date

text: Red Amaranth was grown in the Yamuna soil with addition of chemical fertilizer, DAP. Plantation was done in month of April and harvested in June.

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: Delhi

characteristic: geographic location (region and locality)

text: plant metagenome

text: plant metagenome


name: SAMIN0003313-Red Amaranth grown with Leaf waste compost in Yamuna soil

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Pooja Sharma, Daulat Ram College, University of Delhi

characteristic: INSDC first public

text: public

text: IBDC

text: Red Amaranth was grown in the Yamuna soil with addition of leaf waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003316-Red Amaranth grown with vermicompost in Yamuna soil

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: IBDC

text: Red Amaranth was grown in the Yamuna soil with addition of vermicompost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003317-Red Amaranth grown with Fertilizer, DAP in Normal soil

characteristic: ENA-LAST-UPDATE

text: public

characteristic: Submitter Id

text: IBDC

characteristic: broker name

text: Red Amaranth was grown in the Normal soil with addition of chemical fertilizer, DAP. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003319-Red Amaranth grown with leaf waste compost in Normal soil

characteristic: External Id

characteristic: INSDC center name

text: public

text: IBDC

text: Red Amaranth was grown in the Normal soil with addition of leaf waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

text: plant metagenome


name: SAMIN0003314-Red Amaranth grown with municipal waste compost in Yamuna soil

text: public

text: IBDC

characteristic: common name

text: Red Amaranth was grown in the Yamuna soil with addition of municipal waste compost. Plantation was done in month of April and harvested in June.

characteristic: description

text: Yes

text: India

text: Department of Biochemistry, Daulat Ram College, University of Delhi

text: plant metagenome

text: plant metagenome


name: SAMIN0003315-Red Amaranth grown with cow dung manure in Yamuna soil

text: public

text: IBDC

text: Red Amaranth was grown in the Yamuna soil with addition of Cow Dung manure. Plantation was done in month of April and harvested in June.

text: Yes

text: India

text: plant metagenome

characteristic: organism

text: plant metagenome

characteristic: title


name: SAMIN0003320-Red Amaranth grown with  cow dung manure in Normal soil

text: public

text: IBDC

text: Red Amaranth was grown in the Normal soil with addition of Cow Dung manure. Plantation was done in month of April and harvested in June.

text: Yes

text: India

characteristic: geographic location (country and/or sea)

text: plant metagenome

text: plant metagenome


name: SAMIN0003321-Red Amaranth grown with kitchen waste compost in Normal soil

text: public

text: IBDC

text: Red Amaranth was grown in the Normal soil with addition of kitchen waste compost. Plantation was done in month of April and harvested in June.

text: Yes

text: India

characteristic: geographic location (region and locality)

text: plant metagenome

text: plant metagenome


E-MTAB-13033:GCD11 RIP Rep 1

characteristic: ENA-CHECKLIST

text: The University of Manchester

text: public

text: E-MTAB-13033:GCD11 RIP Rep 1

tag: Namespace:The University of Manchester

text: ArrayExpress

text: baker's yeast

text: Protocols: All yeast growth was in synthetic complete dextrose (SCD) media lacking histidine (ForMedium, UK) at 30 o C . BY4741 TAP tagged strains of Gcd11p, Lsm1p, Pat1p, and Prt1p were obtained from Thermo Scientific Open Biosystems (Waltham, MA, USA). Cells were grown to an OD 600 of 0.6 - 0.7, frozen in liquid nitrogen and lysed using a Spex freezer Mill 6870 into Lola140: 20 mM Tris - HCl (pH 8), 140 mM NaCl, 1 mM MgCl 2 , 0.5% NP40, 0.5 mM DTT, 1 mM PMSF, EDTA free Protease Inhibitor cocktail tablet (Roche Diagnostics, Indianaplois, IN, USA), 100 μM NaV 3 O 4 , 5 mM NaF and 40 units/ml RNasin (Promega, Flitchburg, WI, USA). RNA was isolated and purified using Trizol LS reagent (Invitrogen) from input yeast lysate or immunoprecipated TAP tagged protein, quantified using a N anodrop 8000 spectrophotometer (Thermo ) and rRNA depleted . rRNA depletion was confirmed using a Bioanalyzer (Agilent Technologies, CA, USA) Sequencing libraries were then generated using the TruSeq Stranded mRNA sample preparation kit ( Illumina , CA, USA). Total RNA was submitted to the University of Manchester Genomic Technologies Core Facility (GTCF). Quality and integrity of the RNA samples were assessed using a 2200 TapeStation (Agilent Technologies) and then libraries generated using the TruSeq® Stranded mRNA assay (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, rRNA depleted total RNA (0.1-4ug) was used as input material which was fragmented using divalent cations under elevated temperature and then reverse transcribed into first strand cDNA using random primers. Second strand cDNA was then synthesised using DNA Polymerase I and RNase H. Following a single 'A' base addition, adapters were ligated to the cDNA fragments, and the products then purified and enriched by PCR to create the final cDNA library.

characteristic: genotype

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae

characteristic: strain

text: GCD11 RIP Rep 1


E-MTAB-13033:GCD11 RIP Rep 2

characteristic: ENA-FIRST-PUBLIC

text: The University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13033:GCD11 RIP Rep 2

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: GCD11 RIP Rep 2


E-MTAB-13033:GCD11 RIP Rep 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Manchester

characteristic: INSDC center name

text: public

text: E-MTAB-13033:GCD11 RIP Rep 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: GCD11 RIP Rep 3


E-MTAB-13033:LSM1  RIP Rep 1

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 RIP Rep 1

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: not applicable

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: LSM1 RIP Rep 1

characteristic: title


E-MTAB-13033:LSM1  RIP Rep 2

characteristic: ENA-CHECKLIST

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 RIP Rep 2

text: ArrayExpress

text: baker's yeast

characteristic: genotype

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: LSM1 RIP Rep 2


E-MTAB-13033:LSM1  RIP Rep 3

characteristic: ENA-FIRST-PUBLIC

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 RIP Rep 3

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae

characteristic: strain

text: LSM1 RIP Rep 3


E-MTAB-13033:PAT1 RIP Rep 1

text: The University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-13033:PAT1 RIP Rep 1

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PAT1 RIP Rep 1


E-MTAB-13033:PAT1 RIP Rep 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Manchester

text: public

characteristic: SRA accession

text: E-MTAB-13033:PAT1 RIP Rep 2

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PAT1 RIP Rep 2


E-MTAB-13033:PAT1 RIP Rep 3

text: The University of Manchester

characteristic: INSDC center name

text: public

text: E-MTAB-13033:PAT1 RIP Rep 3

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PAT1 RIP Rep 3


E-MTAB-13033:PRT1  RIP Rep 1

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 RIP Rep 1

text: ArrayExpress

text: baker's yeast

characteristic: common name

characteristic: description

text: not applicable

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PRT1 RIP Rep 1


E-MTAB-13033:PRT1  RIP Rep 2

characteristic: ENA-CHECKLIST

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 RIP Rep 2

text: ArrayExpress

text: baker's yeast

characteristic: genotype

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PRT1 RIP Rep 2

characteristic: title


E-MTAB-13033:PRT1  RIP Rep 3

characteristic: ENA-FIRST-PUBLIC

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 RIP Rep 3

text: ArrayExpress

text: baker's yeast

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae

text: PRT1 RIP Rep 3


E-MTAB-13033:GCD11 Total Rep 1

text: The University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13033:GCD11 Total Rep 1

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

characteristic: strain

text: GCD11 Total Rep 1


E-MTAB-13033:GCD11 Total Rep 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Manchester

text: public

characteristic: INSDC status

text: E-MTAB-13033:GCD11 Total Rep 2

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: GCD11 Total Rep 2


E-MTAB-13033:GCD11 Total Rep 3

text: The University of Manchester

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: E-MTAB-13033:GCD11 Total Rep 3

characteristic: Submitter Id

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: GCD11 Total Rep 3


E-MTAB-13033:LSM1  Total Rep 1

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 Total Rep 1

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

characteristic: description

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: LSM1 Total Rep 1


E-MTAB-13033:LSM1  Total Rep 2

characteristic: ENA-CHECKLIST

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 Total Rep 2

text: ArrayExpress

text: baker's yeast

characteristic: genotype

text: not applicable

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: LSM1 Total Rep 2


E-MTAB-13033:LSM1  Total Rep 3

characteristic: ENA-FIRST-PUBLIC

text: The University of Manchester

text: public

text: E-MTAB-13033:LSM1 Total Rep 3

text: ArrayExpress

text: baker's yeast

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: LSM1 Total Rep 3

characteristic: title


E-MTAB-13033:PAT1  Total Rep 1

text: The University of Manchester

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-13033:PAT1 Total Rep 1

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

characteristic: organism part

text: Saccharomyces cerevisiae

text: PAT1 Total Rep 1


E-MTAB-13033:PAT1  Total Rep 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The University of Manchester

text: public

text: E-MTAB-13033:PAT1 Total Rep 2

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

characteristic: strain

text: PAT1 Total Rep 2


E-MTAB-13033:PAT1  Total Rep 3

text: The University of Manchester

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-13033:PAT1 Total Rep 3

text: ArrayExpress

text: baker's yeast

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PAT1 Total Rep 3


E-MTAB-13033:PRT1  Total Rep 1

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 Total Rep 1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: baker's yeast

characteristic: common name

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PRT1 Total Rep 1


E-MTAB-13033:PRT1  Total Rep 2

characteristic: ENA-CHECKLIST

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 Total Rep 2

text: ArrayExpress

text: baker's yeast

characteristic: description

characteristic: genotype

text: not applicable

text: Saccharomyces cerevisiae

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PRT1 Total Rep 2


E-MTAB-13033:PRT1  Total Rep 3

characteristic: ENA-FIRST-PUBLIC

text: The University of Manchester

text: public

text: E-MTAB-13033:PRT1 Total Rep 3

text: ArrayExpress

text: baker's yeast

text: not applicable

characteristic: isolate

text: Saccharomyces cerevisiae

characteristic: organism

text: Saccharomyces cerevisiae

text: whole organism

text: Saccharomyces cerevisiae

text: PRT1 Total Rep 3


characteristic: INSDC first public

characteristic: INSDC last update

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Azores

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Madeira

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Canarias

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Athlit

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Madeira-D

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Java

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Azores-T

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text: Columba livia

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text: Columba livia

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Cyprus

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text: Dried Toepad

text: Cyprus

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Canarias-T

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text: Columba livia

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text: rock pigeon

text: Dried Toepad

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Sudan

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Mali-T

text: Globe Insitute

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text: Mali-T

text: rock pigeon

text: Dried Toepad

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text: Columba livia

text: Columba livia

text: Rock dove


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text: Columba livia

text: Columba livia

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text: Globe Insitute

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text: rock pigeon

text: Dried Toepad

text: Syria

text: Columba livia

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Aden

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text: Dried Toepad

text: Yemen

text: Columba livia

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text: Globe Insitute

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text: Dried Toepad

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text: Columba livia

text: Columba livia

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text: public

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text: Egypt

text: Columba livia

text: Columba livia

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text: Globe Insitute

text: public

text: rock pigeon

text: Dried Toepad

text: United Kingdom

text: Columba livia

text: Columba livia

text: Rock dove


Oman

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text: public

text: Oman

text: rock pigeon

text: Toepad (alcohol)

text: Oman

text: Columba livia

text: Columba livia

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text: INRAE Jouy-en-Josas

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characteristic: broker name

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text: human

text: Protocols: commercial samples obtained from Ambion: Ambion is a brand of life science research products and technologies, mainly focused on RNA products. It is owned by Thermo Fisher Scientific, a company that provides a variety of scientific research products and services. Therefore, \"total RNA commercial samples obtained from Ambion\" refers to RNA samples purchased from this brand for research purposes. SMARTer cDNA library preparation: SMARTer cDNA library preparation is a protocol for long-read sequencing that involves the addition of a poly(A) tail to RNA, followed by reverse transcription using oligo(dT) primers. This results in the synthesis of cDNA with a 5' end that contains a known sequence, which is used for further amplification and sequencing. The SMARTer protocol also incorporates a template switching oligo, which allows for the amplification of full-length cDNA molecules and increases the efficiency of library preparation. KAPA LTP Illumina Library Preparation kit: short read protocol to build libraries starting from full-length cDNA amplicons. The cDNA full-length libraries can be prepared using SMARTer or CapTrap full-length cDNA. The cDNA samples were fragmented using Covaris under the following parameters: 10% Duty cycle, Intensity 5, 200 Cycles per burst, during 30 seconds in a total volume of 55 μl. Illumina sequencing library was prepared using KAPA LTP Library Preparation kit Illumina and the manufacturer protocol was strictly followed. All samples were barcoded and multiplexed using the Illumina barcoding system (6 mers) and then sequenced in a Hi-Seq 2500 lane with HiSeq Sequencing v4 Chemistry.

text: adult

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text: not applicable

characteristic: isolate

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text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: illumina-Crg-Smarter-Brain


text: Centre for Genomic Regulation (CRG)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: missing: third party data

characteristic: collection date

text: human

text: adult

text: normal

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: illumina-Crg-Smarter-Heart

characteristic: title


characteristic: ENA-LAST-UPDATE

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characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: missing: third party data

text: human

text: Protocols: commercial samples obtained from Ambion: Ambion is a brand of life science research products and technologies, mainly focused on RNA products. It is owned by Thermo Fisher Scientific, a company that provides a variety of scientific research products and services. Therefore, \"total RNA commercial samples obtained from Ambion\" refers to RNA samples purchased from this brand for research purposes. DirectRNA library preparation: The DirectRNA library preparation is a long-read sequencing protocol that enables direct sequencing of native RNA molecules. This method involves the enrichment of polyadenylated RNA species and direct cDNA synthesis, resulting in full-length cDNA sequences without the need for fragmentation or amplification. The DirectRNA protocol allows for the identification of alternative splicing events and the detection of RNA modifications.

text: adult

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text: Homo sapiens

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text: Centre for Genomic Regulation (CRG)

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text: male

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text: Centre for Genomic Regulation (CRG)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: missing: third party data

text: human

text: Protocols: commercial samples obtained from Ambion: Ambion is a brand of life science research products and technologies, mainly focused on RNA products. It is owned by Thermo Fisher Scientific, a company that provides a variety of scientific research products and services. Therefore, \"total RNA commercial samples obtained from Ambion\" refers to RNA samples purchased from this brand for research purposes. Teloprime cDNA library preparation: The Teloprime cDNA library preparation method uses the Poly(A) plus Cap-Dependent Linker Ligation (CDLL) protocol. This involves the selection of mRNA with a poly(A) tail, followed by the addition of a cap-dependent linker to the 5' end of the RNA molecule. The RNA is then reverse-transcribed into cDNA, which is subsequently amplified and used for downstream applications such as next-generation sequencing. This method allows for the detection of full-length transcripts and provides an accurate representation of the transcriptome.

text: adult

text: normal

characteristic: disease

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characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: ont-Crg-Telop-Brain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Genomic Regulation (CRG)

text: public

text: ArrayExpress

text: missing: third party data

characteristic: collection date

text: human

text: Protocols: commercial samples obtained from Ambion: Ambion is a brand of life science research products and technologies, mainly focused on RNA products. It is owned by Thermo Fisher Scientific, a company that provides a variety of scientific research products and services. Therefore, \"total RNA commercial samples obtained from Ambion\" refers to RNA samples purchased from this brand for research purposes. CapTrap cDNA library preparation: CapTrap cDNA library preparation is a long-read sequencing protocol that selectively enriches 5'-capped transcripts by capturing the 5' caps of transcripts. This protocol uses Poly(A) tail selection to specifically target mRNA, and a 5' cap-specific oxidation reaction coupled to biotin-streptavidin to capture the 5' cap structure. The captured mRNA is then converted to cDNA and the library is prepared with 5' and 3' specific linkers to enrich for full-length libraries. CapTrap is particularly useful for studying transcription start sites, alternative splicing, and post-transcriptional modifications. Capture Long-Read Sequencing (CLS): The CLS library preparation protocol combines targeted RNA capture using streptavidin and biotin-based probes with third-generation long-read sequencing technologies like ONT and PacBio. This method allows for the preparation of sequencing libraries that can selectively enrich specific regions of the transcriptome, enabling the identification of novel transcripts and splice variants with high accuracy and coverage.

text: adult

text: normal

characteristic: geographic location (country and/or sea)

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text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

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characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

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characteristic: SRA accession

characteristic: Submitter Id

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text: missing: third party data

text: human

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text: Homo sapiens

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text: Homo sapiens

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text: Centre for Genomic Regulation (CRG)

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: broker name

text: missing: third party data

text: human

characteristic: common name

text: Protocols: commercial samples obtained from Ambion: Ambion is a brand of life science research products and technologies, mainly focused on RNA products. It is owned by Thermo Fisher Scientific, a company that provides a variety of scientific research products and services. Therefore, \"total RNA commercial samples obtained from Ambion\" refers to RNA samples purchased from this brand for research purposes. SMARTer cDNA library preparation: SMARTer cDNA library preparation is a protocol for long-read sequencing that involves the addition of a poly(A) tail to RNA, followed by reverse transcription using oligo(dT) primers. This results in the synthesis of cDNA with a 5' end that contains a known sequence, which is used for further amplification and sequencing. The SMARTer protocol also incorporates a template switching oligo, which allows for the amplification of full-length cDNA molecules and increases the efficiency of library preparation.

characteristic: description

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characteristic: developmental stage

text: normal

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre for Genomic Regulation (CRG)

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text: ArrayExpress

text: missing: third party data

text: human

text: adult

text: normal

characteristic: disease

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characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: pacBio-Cshl-CapTrap-Brain