text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: OCT biological replicate 3 from the genotype A2

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


status: PUBLIC

tag: attribute

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characteristic: common name

text: OCT biological replicate 1 from the genotype Y

characteristic: description

text: Populus tremula x Populus tremuloides

characteristic: organism

text: Populus tremula x Populus tremuloides

characteristic: title


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: OCT biological replicate 2 from the genotype Y

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: OCT biological replicate 3 from the genotype Y

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

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text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 2 from the genotype A1

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 3 from the genotype A1

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 1 from the genotype A2

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 2 from the genotype A2

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 3 from the genotype A2

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 1 from the genotype Y

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

text: SEP biological replicate 2 from the genotype Y

text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UPSC

text: public

text: Populus tremula x Populus tremuloides

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text: Populus tremula x Populus tremuloides

text: Populus tremula x Populus tremuloides


text: UNIVERSITY OF WARWICK

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tag: Namespace:UNIVERSITY OF WARWICK

text: Bellum Rainforest Virome 1 Lombong Kelubi

text: Yes

text: Malaysia

characteristic: geographic location (country and/or sea)

text: soil metagenome

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text: UNIVERSITY OF WARWICK

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text: Yes

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text: UNIVERSITY OF WARWICK

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text: Yes

text: Malaysia

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text: UNIVERSITY OF WARWICK

text: public

text: Bellum Rainforest Virome 4 Water Trumpet

text: Yes

text: Malaysia

text: soil metagenome

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text: Bellum Rainforest Virome 4


text: UNIVERSITY OF WARWICK

text: public

text: Bellum Rainforest Virome 5 Water Trumpet

text: Yes

text: Malaysia

text: soil metagenome

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text: UNIVERSITY OF WARWICK

text: public

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text: CENTER FOR GENOMIC REGULATION (CRG)

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tag: Namespace:CENTER FOR GENOMIC REGULATION (CRG)

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text: Mus musculus musculus

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text: eastern European house mouse

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text: MMS

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text: Phaeodactylum tricornutum

text: Phaeodactylum tricornutum

characteristic: strain


text: public

tag: Namespace:MONASH INSTITUTE OF MEDICAL RESEARCH - MONASH UNIVERSITY

characteristic: collection date

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text: Unsure

characteristic: gastrointestinal tract disorder

text: Australia

unit: DD

characteristic: geographic location (latitude)

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text: human-gut

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characteristic: ENA-CHECKLIST

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text: Continuous arable wheat treatment

characteristic: current land use

text: Winter wheat Triticum aestivum L., cv. Hereward

characteristic: current vegetation

text: KEGG k04561 selected Sequences from bulk soil DNA Metagenome sampled October 2011 from long-term Continuous arable treatment since 1949

characteristic: description

text: Soil

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (country and/or sea)

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characteristic: geographic location (depth)

characteristic: geographic location (elevation)

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text: Hertfordshire, Harpenden, Rothamsted Research, Highfield Ley-Arable Experiment

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characteristic: history/crop rotation

text: metagenome

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characteristic: organism

text: Rothamsted Highfield Ley-Arable field soil Metagenomes

text: Bare-fallow, arable and grassland plots on the Highfield/Geescroft site of Rothamsted farm were arranged in a replicated randomized block design to provide three plots for each treatment. All plots except those remaining as permanent grassland were ploughed (standard depth, 23 cm) a few days prior to sampling. Three randomly assigned grid areas were sampled to 10 cm depth using a 3 cm dia. corer with the top 2 cm containing plant detritus discarded. Ten cores for each grid area were pooled and thoroughly mixed and sieved through 2 mm mesh; samples were then processed immediately (e.g. for dry weight estimations) or frozen at ?80 °C for subsequent analysis

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text: soil metagenome

text: pyrosequencing

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text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

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text: Rothamsted Highfield Arable plot 24 bulk soil sample

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characteristic: ENA-CHECKLIST

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characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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characteristic: ENA-CHECKLIST

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text: Soil

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

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characteristic: description

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characteristic: environment (biome)

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text: Soil

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characteristic: geographic location (country and/or sea)

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characteristic: geographic location (country and/or sea)

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characteristic: history/crop rotation

text: metatranscriptome

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text: Rothamsted Highfield Ley-Arable field soil Metagenomes

characteristic: sample collection device or method

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text: soil metagenome

text: pyrosequencing

text: soil

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text: Chromic Luvisol

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characteristic: description

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characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

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text: United Kingdom

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text: metatranscriptome

characteristic: investigation type

text: soil metagenome

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text: Bare-fallow, arable and grassland plots on the Highfield/Geescroft site of Rothamsted farm were arranged in a replicated randomized block design to provide three plots for each treatment. All plots except those remaining as permanent grassland were ploughed (standard depth, 23 cm) a few days prior to sampling. Three randomly assigned grid areas were sampled to 10 cm depth using a 3 cm dia. corer with the top 2 cm containing plant detritus discarded. Ten cores for each grid area were pooled and thoroughly mixed and sieved through 2 mm mesh; samples were then processed immediately (e.g. for dry weight estimations) or frozen at ?80 °C for subsequent analysis

text: soil metagenome

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characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Permanent grassland

text: Grassland mixed sward

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Mixed grass sward since at least 1838

characteristic: history/crop rotation

text: metatranscriptome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Permanent grassland

characteristic: current land use

text: Grassland mixed sward

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Mixed grass sward since at least 1838

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Continuous arable wheat treatment

text: KEGG k10944 selected Sequences from bulk soil DNA Metagenome sampled October 2011 from long-term Continuous arable treatment since 1949

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Continuous Arable since 1949

characteristic: history/crop rotation

text: metagenome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

text: Rothamsted Highfield Arable plot 14 bulk soil sample

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Continuous arable wheat treatment

characteristic: current land use

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Continuous Arable since 1949

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer

text: Rothamsted Highfield Arable plot 20 bulk soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Continuous arable wheat treatment

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Continuous Arable since 1949

characteristic: history/crop rotation

text: metagenome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

text: Rothamsted Highfield Arable plot 24 bulk soil sample

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Bare-fallow

characteristic: current land use

text: Bare-fallow

characteristic: current vegetation

text: KEGG k10944 selected Sequences from Bulk soil DNA Metagenome sampled October 2011 from long-term Bare-fallow treatment since 1959

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Bare-fallow since 1959

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer

text: Rothamsted Highfield Bare-fallow plot 03 bulk soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Bare-fallow

text: Bare-fallow

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Bare-fallow since 1959

characteristic: history/crop rotation

text: metagenome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

text: Rothamsted Highfield Bare-fallow plot 04 bulk soil sample

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Bare-fallow

characteristic: current land use

text: Bare-fallow

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Bare-fallow since 1959

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer

text: Rothamsted Highfield Bare-fallow plot 08 bulk soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Permanent grassland

text: Grassland mixed sward

text: KEGG k10944 selected Sequences from Bulk soil DNA Metagenome sampled October 2011 from long-term grassland since at least 1838

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Mixed grass sward since at least 1838

characteristic: history/crop rotation

text: metagenome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

text: Rothamsted Highfield Grassland plot 10 bulk soil sample

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Permanent grassland

characteristic: current land use

text: Grassland mixed sward

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Mixed grass sward since at least 1838

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer

text: Rothamsted Highfield Grassland plot 17 bulk soil sample


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Permanent grassland

text: Grassland mixed sward

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Mixed grass sward since at least 1838

characteristic: history/crop rotation

text: metagenome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

text: Rothamsted Highfield Grassland plot 26 bulk soil sample

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Continuous arable wheat treatment

characteristic: current land use

text: Winter wheat Triticum aestivum L., cv. Hereward

characteristic: current vegetation

text: KEGG k10944 selected Sequences from bulk soil DNA Metatranscriptome sampled October 2011 from long-term Continuous arable treatment since 1949

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Continuous Arable since 1949

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Continuous arable wheat treatment

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

text: Hertfordshire, Harpenden, Rothamsted Research, Highfield Ley-Arable Experiment

characteristic: geographic location (region and locality)

text: Continuous Arable since 1949

characteristic: history/crop rotation

text: metatranscriptome

text: soil metagenome

characteristic: organism

text: Rothamsted Highfield Ley-Arable field soil Metagenomes

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Continuous arable wheat treatment

characteristic: current land use

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Continuous Arable since 1949

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: Bare-fallow, arable and grassland plots on the Highfield/Geescroft site of Rothamsted farm were arranged in a replicated randomized block design to provide three plots for each treatment. All plots except those remaining as permanent grassland were ploughed (standard depth, 23 cm) a few days prior to sampling. Three randomly assigned grid areas were sampled to 10 cm depth using a 3 cm dia. corer with the top 2 cm containing plant detritus discarded. Ten cores for each grid area were pooled and thoroughly mixed and sieved through 2 mm mesh; samples were then processed immediately (e.g. for dry weight estimations) or frozen at ?80 °C for subsequent analysis

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Bare-fallow

text: Bare-fallow

text: KEGG k10944 selected Sequences from Bulk soil DNA Metatranscriptome sampled October 2011 from long-term Bare-fallow treatment since 1959

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Bare-fallow since 1959

characteristic: history/crop rotation

text: metatranscriptome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Bare-fallow

characteristic: current land use

text: Bare-fallow

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Bare-fallow since 1959

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Bare-fallow

text: Bare-fallow

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Bare-fallow since 1959

characteristic: history/crop rotation

text: metatranscriptome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Permanent grassland

characteristic: current land use

text: Grassland mixed sward

characteristic: current vegetation

text: KEGG k10944 selected Sequences from Bulk soil DNA Metatranscriptome sampled October 2011 from long-term grassland since at least 1838

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Mixed grass sward since at least 1838

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

text: public

text: Permanent grassland

text: Grassland mixed sward

text: Soil

text: Agricultural Land

text: Bulk Soil

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (region and locality)

text: Mixed grass sward since at least 1838

characteristic: history/crop rotation

text: metatranscriptome

text: soil metagenome

characteristic: organism

characteristic: sample collection device or method

characteristic: sample volume or weight for DNA extraction

characteristic: sample weight for DNA extraction

text: soil metagenome

text: pyrosequencing

text: soil

characteristic: soil environmental package

text: Chromic Luvisol

characteristic: soil_taxonomic/FAO classification

text: -80 Freezer

characteristic: storage conditions (fresh/frozen/other)

characteristic: texture

characteristic: title

characteristic: total organic carbon


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: ROTHAMSTED RESEARCH

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Permanent grassland

characteristic: current land use

text: Grassland mixed sward

characteristic: current vegetation

characteristic: description

text: Soil

characteristic: environment (biome)

text: Agricultural Land

characteristic: environment (feature)

text: Bulk Soil

characteristic: environment (material)

text: United Kingdom

characteristic: geographic location (longitude)

text: Mixed grass sward since at least 1838

text: metatranscriptome

characteristic: investigation type

text: soil metagenome

characteristic: project name

text: soil metagenome

text: pyrosequencing

characteristic: sequencing method

text: soil

text: Chromic Luvisol

text: -80 Freezer


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH, BHOPAL

text: Dissected adult testes (10-15 days old)

text: Adult

text: Drosophila albomicans

characteristic: organism

text: Drosophila albomicans

text: Male

characteristic: sex

text: nasuta

text: Testes

text: atac-seq_Drosophila albomicans_testes_replicate1

characteristic: title


text: INDIAN INSTITUTE OF SCIENCE EDUCATION AND RESEARCH, BHOPAL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Dissected adult testes (10-15 days old)

text: Adult

text: Drosophila albomicans

text: Drosophila albomicans

text: Male

text: nasuta

text: Testes

text: atac-seq_Drosophila albomicans_testes_replicate2


text: public

text: Dissected adult testes (10-15 days old)

characteristic: description

text: Adult

text: Drosophila nasuta

text: Drosophila nasuta

text: Male

text: nasuta

text: Testes

text: atac-seq_Drosophila nasuta_testes_replicate1


text: public

text: Dissected adult testes (10-15 days old)

text: Adult

text: Drosophila nasuta

text: Drosophila nasuta

text: Male

text: nasuta

text: Testes

text: atac-seq_Drosophila nasuta_testes_replicate2


E-MTAB-10809:Sample 1

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10809:Sample 1

tag: Namespace:DDG Bioinformatics Sp. z o.o.

text: ArrayExpress

characteristic: broker name

text: Protocols: Single colony of L. monocytogenes EGD-e its derivative mutant strain with inactivated lmo0946 were inoculated in BHI (Oxoid) and grown for 18 hours at 37 ◦C with aeration. RNA protect R Cell Reagent (Qiagen) was added to the cultures’ samples according to the manufacturer’s instructions. Cells were harvested by centrifugation, snap-frozen in liquid nitrogen, and stored at - 80 °C untill further processing. The pellets were re-suspended in 1 mL of TRIGIDITY (Applichem) and cells disrupted by the Minilys® homogenizer (Bertin instruments). Total RNA was subsequently isolated with Direct-zol RNA MiniPrep (ZYMO™) according to the manufacturer’s instructions. To remove DNA contamination, total RNA was incubated with TURBO DNAse (Ambion) in the presence of SUPERase• In™ RNase Inhibitor (Ambion) followed by purification using TURBO DNA- free™ Kit (Ambion). Concentration and assessment of total RNA quality was performed on a NanoDrop and Agilent 2100 Bioanalyzer, respectively. Ribosomal RNA depletion, library preparation and sequencing were performed by Eurofins Genomics Europe Sequencing GmbH. To enrich mRNA and remove ribosomal RNA (rRNA) from total RNA, total RNA was treated with Bacterial rRNA Depletion Kit (NEB). Preparation of cDNA fragment libraries was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Illumina).

text: wild type

characteristic: genetic modification

text: not applicable

characteristic: isolate

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

characteristic: organism part

text: Listeria monocytogenes EGD-e

text: Sample 1


E-MTAB-10809:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10809:Sample 2

text: ArrayExpress

text: wild type

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 2


E-MTAB-10809:Sample 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10809:Sample 3

text: ArrayExpress

text: wild type

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 3


E-MTAB-10809:Sample 4

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10809:Sample 4

text: ArrayExpress

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

characteristic: organism

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 4


E-MTAB-10809:Sample 5

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10809:Sample 5

text: ArrayExpress

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 5

characteristic: title


E-MTAB-10809:Sample 6

text: DDG Bioinformatics Sp. z o.o.

characteristic: INSDC center name

text: public

text: E-MTAB-10809:Sample 6

text: ArrayExpress

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 6


E-MTAB-10810:Sample 1

text: DDG Bioinformatics Sp. z o.o.

characteristic: INSDC first public

text: public

text: E-MTAB-10810:Sample 1

text: ArrayExpress

text: wild type

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 1


E-MTAB-10810:Sample 2

text: DDG Bioinformatics Sp. z o.o.

characteristic: INSDC last update

text: public

text: E-MTAB-10810:Sample 2

text: ArrayExpress

text: wild type

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 2


E-MTAB-10810:Sample 3

text: DDG Bioinformatics Sp. z o.o.

text: public

characteristic: INSDC status

text: E-MTAB-10810:Sample 3

text: ArrayExpress

text: wild type

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 3


E-MTAB-10810:Sample 4

text: DDG Bioinformatics Sp. z o.o.

text: public

characteristic: SRA accession

text: E-MTAB-10810:Sample 4

text: ArrayExpress

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 4


E-MTAB-10810:Sample 5

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10810:Sample 5

characteristic: Submitter Id

text: ArrayExpress

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 5


E-MTAB-10810:Sample 6

text: DDG Bioinformatics Sp. z o.o.

text: public

text: E-MTAB-10810:Sample 6

text: ArrayExpress

characteristic: description

text: inactivation of lmo0946

text: not applicable

text: Listeria monocytogenes EGD-e

text: Listeria monocytogenes EGD-e

text: whole organism

text: Listeria monocytogenes EGD-e

text: Sample 6


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: strain


text: Pseudomonas aeruginosa

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Pseudomonas aeruginosa

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: Klebsiella pneumoniae

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella oxytoca

characteristic: External Id

text: SC

text: public

text: Klebsiella oxytoca

text: Klebsiella oxytoca

text: Klebsiella oxytoca


text: Klebsiella ornithinolytica

text: SC

text: public

text: Klebsiella ornithinolytica

text: Raoultella ornithinolytica

characteristic: organism

text: Raoultella ornithinolytica


text: Klebsiella ornithinolytica

text: SC

text: public

text: Klebsiella ornithinolytica

text: Raoultella ornithinolytica

text: Raoultella ornithinolytica

characteristic: title


text: Klebsiella pneumoniae

text: SC

characteristic: INSDC center name

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella planticola

text: SC

characteristic: INSDC first public

text: public

text: Klebsiella planticola

text: Raoultella planticola

text: Raoultella planticola


text: Klebsiella oxytoca

text: SC

characteristic: INSDC last update

text: public

text: Klebsiella oxytoca

text: Klebsiella oxytoca

text: Klebsiella oxytoca


text: Klebsiella aerogenes

text: SC

text: public

characteristic: INSDC status

text: Klebsiella aerogenes

text: Klebsiella aerogenes

text: Klebsiella aerogenes


text: Klebsiella variicola subsp. variicola

text: SC

text: public

characteristic: SRA accession

text: Klebsiella variicola subsp. variicola

text: Klebsiella variicola subsp. variicola

text: Klebsiella variicola subsp. variicola


text: Klebsiella grimontii

text: SC

text: public

characteristic: Submitter Id

text: Klebsiella grimontii

text: Klebsiella grimontii

text: Klebsiella grimontii


text: Klebsiella michiganensis

text: SC

text: public

text: Klebsiella michiganensis

text: Klebsiella michiganensis

text: Klebsiella michiganensis


text: Klebsiella planticola

text: SC

text: public

text: Klebsiella planticola

text: Raoultella planticola

text: Raoultella planticola


text: Klebsiella michiganensis

text: SC

text: public

text: Klebsiella michiganensis

text: Klebsiella michiganensis

text: Klebsiella michiganensis


text: Klebsiella pasteurii

text: SC

text: public

text: Klebsiella pasteurii

text: Klebsiella pasteurii

text: Klebsiella pasteurii


text: Klebsiella quasipneumaniae subsp. quasipneumoniae

text: SC

text: public

text: Klebsiella quasipneumoniae subsp. quasipneumoniae


text: SC

text: public


text: Klebsiella aerogenes

text: SC

text: public

text: Klebsiella aerogenes

text: Klebsiella aerogenes

text: Klebsiella aerogenes


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella oxytoca

text: SC

text: public

text: Klebsiella oxytoca

text: Klebsiella oxytoca

text: Klebsiella oxytoca


611251834e44802ba4091946:sample:T. suis

text: EI

text: public

characteristic: Source Name

text: 611251834e44802ba4091946:sample:T. suis

text: COPO

characteristic: broker name

text: Trypanosoma suis

text: Trypanosoma suis

text: 611251834e44802ba4091946:sample:T. suis


text: EI

text: public

text: 611251834e44802ba4091946:sample: T. theileri

text: COPO

text: Trypanosoma theileri

text: Trypanosoma theileri


text: EI

text: public

text: 611251834e44802ba4091946:sample: T. pestanai

text: COPO

text: Trypanosoma pestanai

text: Trypanosoma pestanai


text: EI

text: public

text: 611251834e44802ba4091946:sample: T. erneyi

text: COPO

text: Trypanosoma erneyi

text: Trypanosoma erneyi


text: mixed

characteristic: ArrayExpress-SEX

text: Oscheius sp. 2/C/onirici

characteristic: ArrayExpress-SPECIES

text: Mixed

characteristic: GENDER

text: SC

text: public

text: Oscheius sp. 2/C/onirici

characteristic: common name

text: Oscheius onirici

text: Oscheius onirici

text: Oscheius sp. 2/C/onirici


text: mixed

text: Oscheius dolichura

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Mixed

text: SC

text: public

text: Oscheius dolichura

text: Oscheius dolichura

text: Oscheius dolichura

text: Oscheius dolichura


text: mixed

text: Oscheius chongmingensis, cf. wohlgemuthi

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Mixed

text: SC

text: public

text: Oscheius chongmingensis

text: Oscheius chongmingensis


text: DKFZ

text: public

text: ena-upload-cli

text: naked mole-rat

text: DMBA/TPA treated or control back skin and matched livers

characteristic: description

text: Heterocephalus glaber

characteristic: organism

text: Heterocephalus glaber

characteristic: title


text: DKFZ

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ena-upload-cli

text: house mouse

text: Mus musculus

text: Mus musculus


text: DKFZ

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-upload-cli

characteristic: Submitter Id

text: house mouse

text: DMBA or vehicle treated mouse embryonic fibroblasts

text: Mus musculus

text: Mus musculus


text: Enterococcus faecalis

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


text: Enterococcus faecalis

characteristic: ArrayExpress-Species

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis

characteristic: strain


text: Staphylococcus aureus

text: SC

text: public

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus aureus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Staphylococcus aureus

text: Staphylococcus aureus

text: Staphylococcus aureus


text: Staphylococcus haemolyticus

text: SC

text: public

text: Staphylococcus haemolyticus

characteristic: common name

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus


text: Staphylococcus haemolyticus

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus

text: Staphylococcus haemolyticus


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: zebrafish

text: Protocols: HepG2 were obtained from American Type Culture Collection (ATCC, Rockville, MD). The cell line was mycoplasma free when periodically tested with Mycoplasmacheck (Eurofins Genomics). HepG2 were cultured in T75 flasks at 37 °C and 5 % CO2 atmosphere using Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 1/100 Penicillin/Streptomycin (P/S, Sigma) and 10 % fetal bovine serum (Hyclone, GE healthcare). HepG2 cells were maintained by splitting 1/6 three times a week, done by aspirating the medium, gently washing the cells with phosphate buffered saline (PBS, without Mg2+, Sigma) and detaching them with 2 mL of a trypsin-EDTA solution (0.05%, Sigma) for 3-5 min. Trypsin-EDTA was inactivated with a minimum of 10-fold surplus of culture medium before a cell fraction was passaged Substrate preparation: DNAse treated and column cleaned total RNA was fragmeted at 95 degrees celsius in Tris-HCl 80 mM and MgCl2 8 mM final concentrations for 4 minutes and 30 seconds. After fragmentation, the RNA was cleaned using 1 volume of RNA CleanXP Ampure beads and 1 volume of isopropanol; after 2 80% Ethanol washes the RNA was eluted in half the volume of AMPure beads used. 3' dephosphorylation was then performed with T4PNK in TAM buffer (Tris-Acetate 50 mM, Magnesium Chloride 10 mM, pH~8.5) at room temperature for 4 hours followed by AMPure clean-up and subsequently 5' phosphorylated with T4PNK in T4PNK buffer with addition of ATP at 37 degreees celsius for 1 hour according to NEB manufacturer instructions, then AMPure cleaned and aliquoted and stored at -80 degrees celsius until further used. Binding Assay: RBP-Halo fusions are in vitro transcribed and then translated with MegaScript T7 in vitro transcription kit (ThermoFisher) and Wheat Germ extract according to manufacturers instructions (50 ul in vitro translation reaction). The in vitro translated proteins are recovered using 25 ul Magne Halo Ligand beads (Promega) washed and resuspended in PBSN (1X PBS, 0,005% NP-40) with added RNAse A and Turbo DNAse (Thermo). After 1 hour of incubation, the beads are washed 4 times, twice with high salt (PBSN + 1M MgCl2) and twice with normal salt (PBSN). Beads are ruspended in 50 ul of PBSN and mixed with one aliquote of substrate RNA (150 ng in total) brought to room temperature and diluted to a final volume of 50 ul of PBSN. The binding reaction occurs at room temperature for one hour rotating end-over-end subsequently 3 washes in PBSN are performed to remove unbound molecules and elution is perfomed in 15 ul of RNAse free water at 70 degrees celsius for 8 minutes resuspending the beads by pipeting up and down whilst the tube is in the thermocycler for a total of 3 times during the 8 minutes at 70 degrees. 11 ul of the eluted RNA are used to prepare an illumina compatible next generation sequencing library. Upon cell harvest, 700 µL Qiazol (QIAGEN) was directly added onto the cells on ice and mixed. The cell extract was either stored at -80 °C or RNA extraction was continued immediately by adding 140 µL chloroform. This Qiazol/chloroform mixture was shaken for 30 sec and incubated at RT for 3 min, before centrifugation at 9.000 g for 5 min at 4 °C. The upper aqueous phase was transferred to a new tube and an equal volume of isopropanol was added. The tube was inverted 5 times followed by 10 min incubation at RT. The mixture was centrifuged at 9.000 g and 4 °C for 10 min and the supernatant discarded. The pellet was washed in 700 µL cold 70% ethanol and centrifuged at 15.000 g for 5 min at 4 °C. The supernatant was discarded entirely, and the pellet air-dried for 5 minutes, before resuspension in nuclease-free water. RNA concentration was determined by nanodrop (Nanodrop 2000c). RNA was DNase-treated using the Turbo DNase Kit (Thermo Fisher) for 30 min at 37 °C and the reaction was column purified using RNA Clean&Concentrator kit (Zymo Research). The library preparation was carried out using the NEXTFLEX small RNA library preparation kit v3, PerkinElmer catalog # NOVA-5132-06 according to manufacturer instructions. The quality of every cDNA library was determined on an Agilent Bioanalyzer instrument according to the manufacturer’s protocol.

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

characteristic: isolate

text: Danio rerio

text: Danio rerio

text: liver

characteristic: organism part

text: Danio rerio


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, Sweden

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: zebrafish

characteristic: description

text: normal

text: wild type genotype

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: liver

text: Danio rerio

characteristic: title


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: ggHuRHUMAN-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: hepatocyte

text: human

characteristic: common name

text: hepatocellular carcinoma

text: control-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: Halo


text: public

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: zebrafish

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

text: not applicable

text: Danio rerio

text: Danio rerio

text: liver

text: Danio rerio

text: HaloFISH


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: hsHuRHUMAN-HaloTag

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: human

characteristic: description

text: hepatocellular carcinoma

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: INSDC first public

text: public

text: ArrayExpress

text: hepatocyte

text: zebrafish

text: normal

text: wild type genotype

text: not applicable

text: Danio rerio

characteristic: organism

text: Danio rerio

text: liver

text: Danio rerio

text: InputFISH

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: mdHuRHUMAN-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: Submitter Id

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: mmHuRHUMAN-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: human

characteristic: common name

text: hepatocellular carcinoma

characteristic: disease

text: control-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: input DNA-HaloTag

characteristic: genotype

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: xtHuRHUMAN-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens


characteristic: INSDC first public

text: public

text: ArrayExpress

text: hepatocyte

text: human

characteristic: description

text: hepatocellular carcinoma

text: HNRNPC-HaloTag

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: input DNA-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens

text: Input

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: SRA accession

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: MANF-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: hepatocyte

text: human

characteristic: common name

text: hepatocellular carcinoma

text: NASP-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

characteristic: disease

text: PKM-HaloTag

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: hepatocyte

text: human

text: hepatocellular carcinoma

text: RAN-HaloTag

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: liver

text: Homo sapiens


characteristic: INSDC first public

text: public

text: ArrayExpress

text: hepatocyte

text: human

characteristic: description

text: hepatocellular carcinoma

text: TKT-HaloTag

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens


text: Klebsiella pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


text: Klebsiella pneumoniae

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: strain

characteristic: title


text: Klebsiella pneumoniae

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: Submitter Id

text: Klebsiella pneumoniae

characteristic: common name

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Klebsiella pneumoniae

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Bifidobacterium breve

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Bifidobacterium breve

text: Bifidobacterium breve

text: Bifidobacterium breve


text: Enterococcus faecalis

text: SC

characteristic: INSDC last update

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


text: unidentified

text: SC

text: public

characteristic: INSDC status

text: unidentified

text: unidentified

text: unidentified


text: UNIVERSITY OF FREIBURG

text: public

text: ena-upload-cli v0.2.4 @ Galaxy

tag: Namespace:UNIVERSITY OF FREIBURG

text: Institute of test data generation

characteristic: collecting institution

characteristic: collection date

text: me

characteristic: collector name

text: viral

characteristic: description

text: Afghanistan

characteristic: geographic location (country and/or sea)

text: human

characteristic: host common name

text: not applicable

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

characteristic: host subject id

text: abcde

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

text: THE sample


text: Streptococcus agalactiae)

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus agalactiae)

characteristic: common name

text: Streptococcus agalactiae

text: Streptococcus agalactiae

characteristic: title


text: ETH-Zurich

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Abattoir

characteristic: description

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 7

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 8

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 9

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 12

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 13

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Chicken_donor 1

text: chicken gut metagenome

text: chicken gut metagenome

text: Caecal inoculum 1


text: ETH-Zurich

text: public

text: Chicken_donor 2

text: chicken gut metagenome

text: chicken gut metagenome

text: Caecal inoculum 2


text: ETH-Zurich

text: public

text: Day 20

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 21

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 22

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 25

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 26

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 27

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 28

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 29

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 34

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 35

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 36

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 37

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 38

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 44

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 45

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 46

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 54

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 55

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 56

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 57

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 58

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 65

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 66

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 67

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 68

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 69

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 70

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Chicken_donor 3

text: chicken gut metagenome

text: chicken gut metagenome

text: Caecal inoculum 3


text: ETH-Zurich

text: public

text: Day 16

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 17

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 18

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 20

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 21

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 22

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 29

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 30

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 31

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 32

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 33

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 40

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 41

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 42

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 50

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 51

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 52

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 60

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 61

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 62

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 70

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 71

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 72

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 80

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 81

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 82

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 6

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 7

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 8

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 9

text: chicken gut metagenome

text: chicken gut metagenome


text: ETH-Zurich

text: public

text: Day 10

text: chicken gut metagenome

text: chicken gut metagenome


text: Streptococcus pneumoniae

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: TIGR 4

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: Serotype 4

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: Serotype 14

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: Serotype 5

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Streptococcus pneumoniae

text: Serotype 1

text: SC

text: public

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: iPSC

text: not applicable

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Human

text: QIAcube Batch 23

text: Male

characteristic: GENDER

text: SC

text: public

text: not applicable

characteristic: PHENOTYPE

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 24

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 25

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Male

text: SC

characteristic: INSDC center name

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 26

text: Male

text: SC

characteristic: INSDC first public

text: public

text: not applicable

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 27

text: Male

text: SC

characteristic: INSDC last update

text: public

text: not applicable

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: NPC

text: not applicable

text: male

text: Human

characteristic: ArrayExpress-SPECIES

text: QIAcube Batch 28

text: Male

text: SC

text: public

characteristic: INSDC status

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Human

text: QIAcube Batch 32

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 33

text: Male

characteristic: GENDER

text: SC

text: public

text: not applicable

characteristic: PHENOTYPE

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 34

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 35

characteristic: ENA-LAST-UPDATE

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 36

characteristic: External Id

text: Male

text: SC

characteristic: INSDC center name

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 37

text: Male

text: SC

characteristic: INSDC first public

text: public

text: not applicable

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 38

text: Male

text: SC

characteristic: INSDC last update

text: public

text: not applicable

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 29

text: Male

text: SC

text: public

text: not applicable

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: NPC

text: not applicable

text: male

text: Human

characteristic: ArrayExpress-SPECIES

text: QIAcube Batch 30

text: Male

text: SC

text: public

characteristic: INSDC status

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

characteristic: ArrayExpress-PHENOTYPE

text: male

characteristic: ArrayExpress-SEX

text: Human

text: QIAcube Batch 31

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


text: iPSC

text: not applicable

text: male

text: Human

text: QIAcube Batch 39

text: Male

characteristic: GENDER

text: SC

text: public

text: not applicable

characteristic: PHENOTYPE

text: human

text: Homo sapiens

text: Homo sapiens


text: NPC

text: not applicable

text: male

text: Human

text: QIAcube Batch 40

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Male

text: SC

text: public

text: not applicable

text: human

text: Homo sapiens

text: Homo sapiens


E-MTAB-10873:Sample 1

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-10873:Sample 1

tag: Namespace:Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany Junior Research Group Somatic Evolution and Early Detection German Cancer Research Center (DKFZ), Heidelberg, Germany

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: naked mole-rat

text: Protocols: Naked mole rats (Heterocephalus glaber) or mice (Mus musculus, C56BL6/J) were culled by neck decapitation and full-thickness 4 and 1 mm2 dorsal skin biopsies, respectively, were immediately collected. Skin biopsies were incubated in dissociation buffer containing 1.25 mg/ml Collagenase I (Sigma), 0.5 mg/ml Collagenase II (Worthington), 0.5 mg/ml Collagenase IV (Worthington) and 0.1 mg/ml Hyaluronic acid (Sigma) for 3 hours at 37°C, 750 rpm. Enzymes were diluted in a final volume of 0.5 ml Hanks Balanced Salt solution (HBSS) per sample (Invitrogen). After 3 hours 0.5 ml 0.5 % Trypsin (Gibco) was added (to a final concentration 0.25%) and incubated at 37C for an additional 30 min at 750 rpm. The Enzymatic digestion was quenched with HBSS supplemented with 10% fetal calf serum (FCS, Gibco) and the cell suspensions were filtered through 40-µm cell strainers (Grenier Bio-One). The strainers were washed with an additional 2-3 ml HBSS containing 10% FCS and cells pelleted by centrifugation at 300 x g for 8 min at 4°C. Cell pellets were then carefully (using wide-bored P1000 pipet tips) resuspended in 100-200 ul sorting buffer (PBS containing 1 mM EDTA (Invitrogen) and 0.04% BSA (Sigma) and 1 μg/ml propidium iodide (Invitrogen)). Cell suspensions were carefully transferred to low-binding polypropylene FACS tubes. Live cells from each sample were sorted into one 96-well flat-bottom low attachment tissue culture plate well containing 30 ul sorting buffer on a cold plate on an BD FACS Aria 2 Len sorter using a 70 µm nozzle (70 psi). PI was excited with a 561 nm laser and fluorescence was recorded with a 610/20 595LP filter. Cells were gated i) FSC-A vs SSC-A to remove debris ii) SSC-W vs SSC-A to exclude doublets iii) RL780/60-A vs PI-A to exclude auto-fluorescent cells and dead cells (PI positive). Single cell cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ kit (User Guide Version 3) according to the manufacture’s instruction. Quantification of the libraries was carried out using the Qubit dsDNA HS Assay Kit (Life Technologies), and cDNA integrity was assessed using D1000 ScreenTapes (Agilent Technologies).

characteristic: description

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Heterocephalus glaber

characteristic: organism

text: Heterocephalus glaber

text: skin of body

characteristic: organism part

text: Heterocephalus glaber

text: male

characteristic: sex

text: Sample 1


E-MTAB-10873:Sample 2

characteristic: External Id

text: Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany Junior Research Group Somatic Evolution and Early Detection German Cancer Research Center (DKFZ), Heidelberg, Germany

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10873:Sample 2

characteristic: Submitter Id

text: ArrayExpress

text: naked mole-rat

characteristic: common name

text: adult

text: wild type genotype

text: not applicable

text: Heterocephalus glaber

text: Heterocephalus glaber

text: skin of body

text: Heterocephalus glaber

text: male

text: Sample 2

characteristic: title


E-MTAB-10873:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-10873:Sample 3

characteristic: age

text: ArrayExpress

characteristic: broker name

text: naked mole-rat

characteristic: description

text: adult

text: wild type genotype

text: not applicable

text: Heterocephalus glaber

text: Heterocephalus glaber

text: skin of body

text: Heterocephalus glaber

text: male

text: Sample 3


E-MTAB-10873:Sample 4

text: public

text: E-MTAB-10873:Sample 4

text: ArrayExpress

text: naked mole-rat

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: not applicable

characteristic: isolate

text: Heterocephalus glaber

characteristic: organism

text: Heterocephalus glaber

text: skin of body

characteristic: organism part

text: Heterocephalus glaber

text: male

text: Sample 4