characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (latitude)

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: sequencing method

text: TLR7.Survival.WT.W12.3S22.RelatedToFigure.2


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: mouse gut metagenome

characteristic: organism

text: A diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity.

characteristic: project name

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W12.3S23.RelatedToFigure.2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (latitude)

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: sequencing method

text: TLR7.Survival.WT.W16.3S21.RelatedToFigure.2


characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W16.3S22.RelatedToFigure.2


text: YALE

text: public

text: mouse

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

characteristic: investigation type

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W16.3S23.RelatedToFigure.2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

text: mouse gut metagenome

characteristic: project name

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W20.3S21.RelatedToFigure.2

characteristic: title


characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (latitude)

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: sequencing method

text: TLR7.Survival.WT.W20.3S22.RelatedToFigure.2


text: YALE

text: public

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W20.3S23.RelatedToFigure.2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

characteristic: investigation type

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W24.3S21.RelatedToFigure.2


characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: mouse

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

text: mouse gut metagenome

characteristic: project name

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W24.3S22.RelatedToFigure.2

characteristic: title


text: YALE

text: public

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: sequencing method

text: TLR7.Survival.WT.W24.3S23.RelatedToFigure.2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W4.3S21.RelatedToFigure.2


characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: mouse

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

characteristic: investigation type

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W4.3S22.RelatedToFigure.2


text: YALE

text: public

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

text: mouse gut metagenome

characteristic: project name

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W4.3S23.RelatedToFigure.2

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (latitude)

text: host-associated

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: sequencing method

text: TLR7.Survival.WT.W8.3S21.RelatedToFigure.2


characteristic: ENA-CHECKLIST

text: YALE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: mouse

text: large intestine

text: fecal material

text: USA

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: metagenome

text: mouse gut metagenome

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W8.3S22.RelatedToFigure.2


text: YALE

text: public

characteristic: collection date

text: mouse

characteristic: environment (biome)

text: large intestine

characteristic: environment (feature)

text: fecal material

characteristic: environment (material)

text: USA

characteristic: geographic location (country and/or sea)

text: host-associated

text: metagenome

characteristic: investigation type

text: mouse gut metagenome

characteristic: organism

text: mouse gut metagenome

text: Illumina MiSeq sequencing

text: TLR7.Survival.WT.W8.3S23.RelatedToFigure.2


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: YALE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: mouse

text: large intestine

text: fecal material

text: USA

text: host-associated

text: metagenome

text: mouse gut metagenome

text: A diet-sensitive commensal Lactobacillus strain mediates TLR7-dependent systemic autoimmunity.

characteristic: project name

text: mouse gut metagenome

text: Illumina MiSeq sequencing

characteristic: title


Deepbinner amplicon read set

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF MELBOURNE

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Deepbinner amplicon read set

tag: Namespace:UNIVERSITY OF MELBOURNE

characteristic: Submitter Id

text: This is a barcoded Oxford Nanopore read set of 12 amplicons that are easily distinguished based on their sequence.

characteristic: description

text: synthetic metagenome

text: synthetic metagenome

text: Deepbinner amplicon read set


Deepbinner WGS read set

text: UNIVERSITY OF MELBOURNE

text: public

text: Deepbinner WGS read set

text: This is a barcoded Oxford Nanopore read set of 12 whole bacterial genomes, each from a different species.

text: synthetic metagenome

text: synthetic metagenome

text: Deepbinner WGS read set


Deepbinner negative control read set

text: UNIVERSITY OF MELBOURNE

text: public

text: Deepbinner negative control read set

text: This is a non-barcoded Oxford Nanopore WGS read set from a Klebsiella pneumoniae genome.

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Deepbinner negative control read set


text: CENTRE FOR GEOGENETICS

text: public

tag: Namespace:CENTRE FOR GEOGENETICS

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: public

tag: Namespace:VTT Technical Research Centre of Finland Ltd

characteristic: collection date

text: deep subsurface

characteristic: environment (biome)

text: crystalline bedrock

characteristic: environment (feature)

text: groundwater

characteristic: environment (material)

text: Finland

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: uncultured bacterium

text: uncultured bacterium

text: 454 GS FLX Titanium

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: VTT Technical Research Centre of Finland Ltd

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: deep subsurface

text: crystalline bedrock

text: groundwater

text: Finland

text: mimarks-survey

characteristic: investigation type

text: uncultured bacterium

characteristic: organism

characteristic: project name

text: uncultured bacterium

text: 454 GS FLX Titanium

characteristic: title

text: water


characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: deep subsurface

characteristic: environment (biome)

text: crystalline bedrock

characteristic: environment (feature)

text: groundwater

characteristic: environment (material)

text: Finland

text: mimarks-survey

text: uncultured archaeon

text: uncultured archaeon

text: 454 GS FLX Titanium

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: deep subsurface

text: crystalline bedrock

text: groundwater

text: Yes

characteristic: environmental sample

text: Finland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: uncultured bacterium

text: 8f, P2

characteristic: pcr primers

text: slow cont pumping, anaerobic cabinet, sterile bottle, filtration

characteristic: sample collection device or method

text: uncultured bacterium

text: 16S rRNA

characteristic: target gene

characteristic: target subfragment


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: deep subsurface

text: crystalline bedrock

text: groundwater

text: Yes

text: Finland

text: uncultured archaeon

characteristic: organism

text: A344f, A744r

text: uncultured archaeon

text: 16S rRNA

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: PERIO-UKM

text: public

characteristic: Submitter Id

text: human oral metagenome

text: human oral metagenome

text: human oral metataxonomics


text: gut metagenome

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: gut metagenome

characteristic: common name

text: gut metagenome

text: gut metagenome

characteristic: subject id


text: INRA

text: public

text: Roseburia intestinalis L1-82 complete genome

characteristic: description

text: Roseburia intestinalis L1-82

text: Roseburia intestinalis L1-82

characteristic: strain

text: Roseburia intestinalis L1-82


text: all cell types

text: whole synchronised population

text: wild-type

characteristic: ArrayExpress-PHENOTYPE

text: hermaphrodite

characteristic: ArrayExpress-SEX

text: Caenorhabditis elegans

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Caenorhabditis elegans

text: Hermaphrodite

characteristic: gender

text: Caenorhabditis elegans

text: wild-type

characteristic: phenotype

text: Caenorhabditis elegans

text: Caenorhabditis elegans


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Laboratory for Immunogenetics, Center for Integrative Medical Sciences

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Mice were maintained on a 12 hr light / dark cycle in a temperature-controlled (22ºC) barrier facility with free access to water and a normal diet (NCD, CA-1, CLEA Japan, Inc.). Isogen II extraction of total RNA was performed according to the manufacturer's instructions. 1 µg of total RNA was used for RNA-seq library preparation with TruSeq Stranded mRNA LT Sample Prep Kit (Illumina), according to the manufacturer’s protocol.

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: liver-specific Cnot1 knockout

text: Mus musculus

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Laboratory for Immunogenetics, Center for Integrative Medical Sciences

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: liver-specific Cnot1 knockout

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: liver

text: liver-specific Cnot1 knockout

characteristic: phenotype

text: Mus musculus

text: male

characteristic: strain


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Mus musculus

text: Mus musculus

text: liver

text: liver-specific Cnot3 knockout

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: house mouse

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: liver

characteristic: organism part

text: wild type

text: Mus musculus

text: female

characteristic: sex


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

text: wild type

text: Mus musculus

text: male


characteristic: ENA checklist

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SSI

characteristic: INSDC center name

text: public

text: Statens Serum Institute

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Denmark

characteristic: geographic location

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: not collected

characteristic: host health state

text: Homo Sapiens

characteristic: host scientific name

text: Yes

characteristic: is the sequenced pathogen host associated?

characteristic: isolate

text: Salmonella enterica

text: Salmonella enterica

text: Kottbus

characteristic: serovar

text: not ascertainable

characteristic: travel-relation


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:CENTER FOR BIOTECHNOLOGY, BIELEFELD UNIVERSITY

characteristic: Submitter Id

text: Vitis riparia x Vitis cinerea

characteristic: organism

text: Vitis riparia x Vitis cinerea

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF LEICESTER

characteristic: INSDC center name

text: public

tag: Namespace:UNIVERSITY OF LEICESTER

text: human

characteristic: common name

text: Sample from 1000 Genomes Project, genomic DNA extracted from a lymphoblastoid cell line from an ACB Afro-Caribbean individual.

characteristic: description

text: Homo sapiens

text: Homo sapiens


text: James Hutton Institute

text: public

tag: Namespace:James Hutton Institute

text: potato

text: RenSeq on P55/7 resistant parent

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: RenSeq on Picasso susceptible parent

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: RenSeq on Resistant Bulk

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: RenSeq on Susceptible Bulk

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: GenSeq on P55/7 resistant parent

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: GenSeq on Picasso susceptible parent

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: GenSeq on Resistant Bulk

text: Solanum tuberosum

text: Solanum tuberosum


text: James Hutton Institute

text: public

text: potato

text: GenSeq on Susceptible Bulk

text: Solanum tuberosum

text: Solanum tuberosum


E-MTAB-7131:Sample 27

text: public

text: E-MTAB-7131:Sample 27

tag: Namespace:Bologna University DISTAL Animal Genomics Division

unit: day

characteristic: age

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

text: Protocols: A total of 48 Italian Large White pigs, 24 gilts and 24 barrows, were used for this study. The pigs were selected from a progeny of 258 piglets derived from 21 sows and 3 boars registered to the herd book of the Italian National Association of Pig Breeders (ANAS). All animals used in this study were kept according to the Council Rule (EC) No 1/2005 on the protection of animals during transport and related operations and amending Directives 64/432/EEC and 93/119/EC and Regulation (EC) No 1255/97. After weaning, at the average live weight of 79.9 ± 5.8 kg, the pigs were divided into 4 groups of 12 animals each, balanced for weight, father and sex. Pigs after weaning were all fed a standard diet until the starting of the trial. During the trial period, the pigs were fed four experimental diets: a standard diet for growing-finishing pigs (D1); a diet enriched with extruded linseed (source of n-3 PUFA) (D2); a diet enriched with extruded linseed, and vitamin E and selenium as antioxidants (D3); a diet enriched with extruded linseed and plant extract from grape-skin and oregano (source of polyphenols) (D4). During the trial, one pig belonging to the experimental group fed D4 died of natural causes (sample 48). At the end of the trial, the animals were transported to a commercial abattoir. At the slaughterhouse, the pigs were electrical stunned and bled in a lying position in agreement with the Council Regulation (EC) No 1099/2009 on the protection of animals at the time of the killing. All slaughter procedures were monitored by the Veterinary team appointed by the Italian Ministry of Health. Slaughter was performed in two batches at a interval of 14 days one from the other. In order to have a similar weight for all the pigs at slaughter, in the first batch were sent the 6 heaviest pigs of each group, for a total of 24 animals. The remaining 6 pigs of each dietary group were then sent in the second batch after 14 days (23 pigs in the second batch as one died before the end of the experiment). Animals of each batch were loaded and transported together in the same truck. Groups were maintained separated inside the truck and during all the pre-slaughter procedures to avoid stress response due to unfamiliar pig mixing. At the end of the slaughter line and before the carcass cooling, a sample from the Longissimus thoracis muscle of each pig was taken and immediately frozen in liquid nitrogen. Samples were then stored at -80°C until RNA extraction. Total RNA was extracted using the standard RNA extraction method with TRIzol (Invitrogen, Carlsbad, CA, USA). Before use, RNA concentration in each sample was assayed with an ND-1000 spectrophotometer (NanoDrop Technologies) and its quality assessed with the Agilent 2100 Bioanalyzer with Agilent RNA 6000 nano kit (Agilent Technologies, Santa Clara, CA, USA). Indexed libraries were prepared from 1 µg of purified RNA from each sample with TruSeq Stranded mRNA (Illumina) Library Prep Kit according to the manufacturer’s instructions. Libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies) and pooled (16 samples/pool for a total of 3 pools) such that each index-tagged sample was present in equimolar amounts, with a final concentration of the pooled samples of 2nM.

text: D1 - standard diet

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: male

characteristic: sex

text: Sample 27


E-MTAB-7131:Sample 30

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Bologna University DISTAL Animal Genomics Division

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-7131:Sample 30

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 30


E-MTAB-7131:Sample 4

characteristic: ENA-LAST-UPDATE

text: public

characteristic: SRA accession

text: E-MTAB-7131:Sample 4

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 4

characteristic: title


E-MTAB-7131:Sample 5

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 5

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

characteristic: description

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 5


E-MTAB-7131:Sample 32

text: public

text: E-MTAB-7131:Sample 32

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

text: D2 - standard diet enriched with extruded linseed

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 32


E-MTAB-7131:Sample 33

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 33

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

characteristic: sex

text: Sample 33


E-MTAB-7131:Sample 35

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 35

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 35


E-MTAB-7131:Sample 8

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 8

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 8

characteristic: title


E-MTAB-7131:Sample 9

text: public

text: E-MTAB-7131:Sample 9

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 9


E-MTAB-7131:Sample 13

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 13

text: Italian Large White

text: ArrayExpress

text: pig

text: D3 - standard diet enriched with extruded linseed and vitamin E and Selenium

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: male

text: Sample 13


E-MTAB-7131:Sample 14

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 14

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

characteristic: sex

text: Sample 14


E-MTAB-7131:Sample 15

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 15

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 15


E-MTAB-7131:Sample 39

text: public

text: E-MTAB-7131:Sample 39

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 39

characteristic: title


E-MTAB-7131:Sample 24

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 24

text: Italian Large White

text: ArrayExpress

text: pig

text: D4 - standard diet enriched with extruded linseed and plant extract from grape-skin and oregano

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 24


E-MTAB-7131:Sample 45

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 45

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 45


E-MTAB-7131:Sample 46

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 46

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

characteristic: sex

text: Sample 46


E-MTAB-7131:Sample 2

text: public

text: E-MTAB-7131:Sample 2

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: D1 - standard diet

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 2


E-MTAB-7131:Sample 28

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 28

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 28

characteristic: title


E-MTAB-7131:Sample 29

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 29

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 29


E-MTAB-7131:Sample 7

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 7

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 7


E-MTAB-7131:Sample 31

text: public

text: E-MTAB-7131:Sample 31

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

characteristic: sex

text: Sample 31


E-MTAB-7131:Sample 36

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 36

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 36


E-MTAB-7131:Sample 37

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 37

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 37

characteristic: title


E-MTAB-7131:Sample 40

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 40

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 40


E-MTAB-7131:Sample 41

text: public

text: E-MTAB-7131:Sample 41

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: male

text: Sample 41


E-MTAB-7131:Sample 42

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 42

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

characteristic: sex

text: Sample 42


E-MTAB-7131:Sample 19

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 19

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 19


E-MTAB-7131:Sample 43

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 43

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 43

characteristic: title


E-MTAB-7131:Sample 44

text: public

text: E-MTAB-7131:Sample 44

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 44


E-MTAB-7131:Sample 47

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 47

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: male

text: Sample 47


E-MTAB-7131:Sample 1

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 1

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

characteristic: sex

text: Sample 1


E-MTAB-7131:Sample 25

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 25

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: D1 - standard diet

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 25


E-MTAB-7131:Sample 26

text: public

text: E-MTAB-7131:Sample 26

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: D1 - standard diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 26

characteristic: title


E-MTAB-7131:Sample 3

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 3

text: Italian Large White

text: ArrayExpress

text: pig

text: D1 - standard diet

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 3


E-MTAB-7131:Sample 10

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 10

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 10


E-MTAB-7131:Sample 11

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 11

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

characteristic: sex

text: Sample 11


E-MTAB-7131:Sample 12

text: public

text: E-MTAB-7131:Sample 12

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 12


E-MTAB-7131:Sample 34

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 34

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 34

characteristic: title


E-MTAB-7131:Sample 6

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 6

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 6


E-MTAB-7131:Sample 16

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 16

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 16


E-MTAB-7131:Sample 17

text: public

text: E-MTAB-7131:Sample 17

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

characteristic: sex

text: Sample 17


E-MTAB-7131:Sample 18

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 18

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 18


E-MTAB-7131:Sample 38

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 38

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: female

text: Sample 38

characteristic: title


E-MTAB-7131:Sample 20

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 20

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

characteristic: diet

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 20


E-MTAB-7131:Sample 21

text: public

text: E-MTAB-7131:Sample 21

characteristic: block

text: Italian Large White

characteristic: breed

text: ArrayExpress

characteristic: broker name

text: pig

characteristic: description

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

characteristic: organism part

text: Sus scrofa

text: female

text: Sample 21


E-MTAB-7131:Sample 22

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-7131:Sample 22

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

characteristic: sex

text: Sample 22


E-MTAB-7131:Sample 23

characteristic: ENA-LAST-UPDATE

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-7131:Sample 23

characteristic: Submitter Id

text: Italian Large White

text: ArrayExpress

text: pig

text: Sus scrofa

characteristic: organism

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 23


E-MTAB-7131:Sample 48

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-7131:Sample 48

characteristic: age

text: Italian Large White

text: ArrayExpress

text: pig

characteristic: common name

text: Sus scrofa

text: Sus scrofa

text: longissimus thoracic muscle

text: Sus scrofa

text: male

text: Sample 48

characteristic: title


Ra

text: EBI

text: public

text: Ra

text: fruit fly

text: Control population was randomly bread between 2 and 30 days post eclosion.

characteristic: description

text: adult

characteristic: dev stage

text: USA

characteristic: geographic location (country and/or sea)

text: Michigan

characteristic: geographic location (region and locality)

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

text: Control population Ra


Rb

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: EBI

characteristic: INSDC first public

text: public

text: Rb

text: fruit fly

text: adult

text: USA

text: Michigan

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

text: Control population Rb


La

characteristic: ENA-LAST-UPDATE

text: EBI

characteristic: INSDC last update

text: public

text: La

text: fruit fly

text: Population selected for postponed senescence by only allowing the 20 - 30% longest living individuals to contribute to the next generation.

text: adult

text: USA

text: Michigan

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

characteristic: sex

text: Selected population La


Lb

text: EBI

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Lb

characteristic: Submitter Id

text: fruit fly

text: adult

text: USA

text: Michigan

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

text: Selected population Lb


characteristic: External Id

text: EBI

characteristic: INSDC center name

text: public

text: fruit fly

text: adult

text: USA

text: Michigan

text: Drosophila melanogaster

characteristic: organism

text: Drosophila melanogaster

text: female

text: Selected population 2La


text: EBI

text: public

text: fruit fly

characteristic: common name

text: adult

text: USA

text: Michigan

text: Drosophila melanogaster

text: Drosophila melanogaster

text: female

text: Selected population 2Lb

characteristic: title


text: Stylephorus chordatus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: tube-eye

text: Stylephorus chordatus

text: Stylephorus chordatus

characteristic: subject id


text: Artedidraco skottsbergi

text: SC

text: public

text: Artedidraco skottsbergi

text: Artedidraco skottsbergi

text: Artedidraco skottsbergi


text: UNIVERSIDAD DE CORDOBA

text: public

tag: Namespace:UNIVERSIDAD DE CORDOBA

characteristic: collection date

text: Holm oak

text: Total DNA soil

characteristic: description

text: dehesa

characteristic: environment (biome)

text: Holm oak rhizosphere

characteristic: environment (feature)

text: Soil

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Quercus ilex

text: NGS Red Seda

characteristic: project name

text: Quercus ilex

text: Illumina MiSeq

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: SOIL


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CNGB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: CNSA

characteristic: broker name

text: Lijiang

characteristic: geographic location

text: 27.167 N, 100.167 E

characteristic: latitude and longitude

text: soil metagenome

characteristic: organism

characteristic: sample name

text: soil metagenome

characteristic: title


text: CNGB

text: public

text: CNSA

characteristic: collection date

characteristic: description

text: Ailaoshan

text: 24.533 N, 101.016 E

text: soil metagenome

text: soil metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: CNGB

text: public

text: CNSA

text: Nabanhe

text: 21.612 N, 101.574 E

text: soil metagenome

text: soil metagenome


text: Pseudomonas aeruginosa MPAO1

characteristic: ArrayExpress-SPECIES

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Pseudomonas aeruginosa MPAO1

characteristic: common name

text: Pseudomonas aeruginosa MPAO1/P1

text: Pseudomonas aeruginosa MPAO1/P1

characteristic: subject id


text: Streptococcus pneumoniae

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: NIOO KNAW

text: public

tag: Namespace:NIOO KNAW

characteristic: Submitter Id

characteristic: environment (biome)

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Netherlands

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: 52o04' N

characteristic: geographic location (latitude)

text: 05o44' E

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: soil metagenome

characteristic: organism

text: Sieving experiment

characteristic: project name

text: soil metagenome

text: Illumina Miseq PE2x250

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: DilutionSamples


characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: common name

text: Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150

characteristic: subject id

characteristic: title


text: Salmonella enterica subsp. enterica serovar Paratyphi A

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae


text: ROTHAMSTED RESEARCH

text: public

tag: Namespace:ROTHAMSTED RESEARCH

text: bread wheat

text: leaf tissue from healthy, untreated 17 days old wheat

characteristic: description

text: Triticum aestivum

text: Triticum aestivum

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: bread wheat

text: wheat cv. Bobwhite leaves sampled at 4 days post mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: bread wheat

text: wheat cv. Bobwhite leaves sampled at 9 days post mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: bread wheat

text: wheat cv. Bobwhite leaves sampled at 13 days post mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: bread wheat

text: wheat cv. Bobwhite leaves sampled at 21 days post mock inoculation

text: Triticum aestivum

text: Triticum aestivum

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: wheat cv. Bobwhite leaves sampled at 4 days post inoculation with Z. tritici IPO323

text: Zymoseptoria tritici IPO323

text: Zymoseptoria tritici IPO323

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: wheat cv. Bobwhite leaves sampled at 9 days post inoculation with Z. tritici IPO323

text: Zymoseptoria tritici IPO323

text: Zymoseptoria tritici IPO323

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: wheat cv. Bobwhite leaves sampled at 13 days post inoculation with Z. tritici IPO323

text: Zymoseptoria tritici IPO323

text: Zymoseptoria tritici IPO323

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: wheat cv. Bobwhite leaves sampled at 21 days post inoculation with Z. tritici IPO323

text: Zymoseptoria tritici IPO323

text: Zymoseptoria tritici IPO323

text: small RNA samples


text: ROTHAMSTED RESEARCH

text: public

text: Z. tritici IPO323 cultured in vitro

text: Zymoseptoria tritici IPO323

text: Zymoseptoria tritici IPO323

text: small RNA samples


text: public

tag: Namespace:Department of Chemistry University of Cambridge

text: ArrayExpress

characteristic: broker name

text: HeLa

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

text: Protocols: HeLa cells were washed in cold PBS and harvested by scraping into cold PBS followed by centrifugation at 300 x g. DNA from up to 10^6 cells was extracted using a Quick-DNA™ kit (Zymo Research) according to the manufacturer's instructions. Genomic lysis buffer was supplemented with TEMPO (20 mM) to minimise the introduction of oxidative damage and DNA was eluted in Tris-HCl buffer (pH 7.4, 10 mM). Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.

text: cervical adenocarcinoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Chemistry University of Cambridge

characteristic: INSDC center name

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: cervical adenocarcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

characteristic: common name

text: Protocols: HeLa cells were washed in cold PBS and harvested by scraping into cold PBS followed by centrifugation at 300 x g. DNA from up to 10^6 cells was extracted using a Quick-DNA™ kit (Zymo Research) according to the manufacturer's instructions. Genomic lysis buffer was supplemented with TEMPO (20 mM) to minimise the introduction of oxidative damage and DNA was eluted in Tris-HCl buffer (pH 7.4, 10 mM). Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR.

text: cervical adenocarcinoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: uterine cervix

text: Homo sapiens

characteristic: title


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: HeLa

text: epithelial cell

text: human

text: Protocols: HeLa cells were washed in cold PBS and harvested by scraping into cold PBS followed by centrifugation at 300 x g. DNA from up to 10^6 cells was extracted using a Quick-DNA™ kit (Zymo Research) according to the manufacturer's instructions. Genomic lysis buffer was supplemented with TEMPO (20 mM) to minimise the introduction of oxidative damage and DNA was eluted in Tris-HCl buffer (pH 7.4, 10 mM). Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR. Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.

text: cervical adenocarcinoma

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: uterine cervix

text: Homo sapiens


text: public

text: ArrayExpress

characteristic: broker name

text: Protocols: Leishmania DNA was purchased from ATCC (product 30012D, lot 62762024). Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.

characteristic: description

text: wild type genotype

text: Leishmania major

text: Leishmania major

text: whole organism

text: Leishmania major


text: public

text: ArrayExpress

text: Protocols: Leishmania DNA was purchased from ATCC (product 30012D, lot 62762024). Purified and sonicated DNA was treated with SMUG1 (25 U, NEB) for 18 hr at 37 °C in the presence of BSA (100 μg/mL). Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR.

text: wild type genotype

characteristic: genotype

text: Leishmania major

text: Leishmania major

text: whole organism

text: Leishmania major


text: public

text: ArrayExpress

text: Protocols: Leishmania DNA was purchased from ATCC (product 30012D, lot 62762024). Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR.

text: wild type genotype

text: Leishmania major

text: Leishmania major

text: whole organism

characteristic: organism part

text: Leishmania major


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

text: Protocols: Leishmania DNA was purchased from ATCC (product 30012D, lot 62762024). Purified and sonicated DNA was treated with UNG (10 U, NEB) for 18 hr at 37 °C. Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.

text: wild type genotype

text: Leishmania major

text: Leishmania major

text: whole organism

text: Leishmania major


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: Protocols: Leishmania DNA was purchased from ATCC (product 30012D, lot 62762024). Purified and sonicated DNA was treated with UNG (10 U, NEB) for 18 hr at 37 °C. Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR.

text: wild type genotype

text: Leishmania major

text: Leishmania major

text: whole organism

text: Leishmania major


characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: Protocols: Synthetic DNA was generated by primer extension using template oligos (see methods section for sequences) Detailed protocol is available in methods section. Briefly, purified DNA was sonicated using a Covaris M220 system, to an average length of 450 bp. Sonicated DNA was treated with HIPS probe 1 (10 mM, 2 hr, RT) and biotinylated using the CuAAC reaction and biotin-PEG3-azide (2 hr, 37 °C). A custom P7 adapter was introduced onto DNA by ligation using a NEBNext Ultra II kit. Labelled DNA was isolated using magnetic streptavidin beads and unbound DNA was removed by washing. The enriched DNA was denatured on the beads using NaOH solution (RT) and then eluted using NaOH solution (70 °C). Eluted DNA was purified once again on magnetic streptavidin beads to remove any non-specific elution. A single primer extension was performed on eluted ssDNA, then a custom P5 adapter was introduced by ligation. Libraries were amplified by PCR.

text: synthetic construct

text: synthetic construct

text: synthetic construct


characteristic: External Id

text: public

text: ArrayExpress

text: Protocols: Synthetic DNA was generated by primer extension using template oligos (see methods section for sequences) Input libraries were prepared for each enriched (snAP-seq) library. DNA was end-prepped using an NEBNext Ultra II kit, followed by adapter ligation using Truseq LT indexed adapters (Illumina). PCR amplification conditions were kept consistent with corresponding enriched (snAP-seq) libraries.

text: synthetic construct

text: synthetic construct

text: synthetic construct


text: IMPERIAL COLLEGE LONDON

characteristic: INSDC center name

text: public

tag: Namespace:IMPERIAL COLLEGE LONDON

text: Please see associated paper - The Mechanism of Resistance to Favipiravir in Influenza

text: Influenza A virus (A/Victoria/3/1975(H3N2))

text: Primer ID sequencing to determine mutations caused by favipiravir for mutant polymerases.


characteristic: INSDC first public

text: public

text: Setd5 delta-SET Homozygous Knock out

characteristic: IndividualGeneticCharacteristics

tag: Namespace:EUROPEAN MOLECUALR BIOLOGY LABORATORY, GENOME BIOLOGY UNIT

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: Protocols : Growth Protocol: For Setd5, PolII, and Hdac3 each replicate 100 million ESCs were harvested and cross linked in 1.5 mM EGS in phosphate-buffered saline (PBS) for 1h followed by 10 min cross linking in 1.5% paraformaldehyde (PFA) in PBS at room temperature. For H3K27ac and H4pan acetyl 20million cells were harvested and crosslinked in 1% PFA for 10 minutes. Cross-linking solution was quenched with 125 mM Glycine for 5 min. Fixed cells were spun down and washed twice with ice cold PBS freshly supplemented with protease inhibitors.Samples were snap frozen in liquid nitrogen and stored at -80C. Chromatin was prepared by re-suspending cross linked cells in hypotonic buffer on ice, followed douncing with a tissue homogenize. Samples were spun down and nuclear pellets were re-suspended in MNase digestion buffer. MNase digestion was performed at for 5 minutes 37C. MNase enzymatic activity was quenched by adding EDTA/EGTA based quenching buffer. Digested chromatin was sonicated with 3 cycles of sonicator at 4C.Samples were spun down to separate insoluble chromatin. Soluble fragmented chromatin was used as ChIP input. Both soluble input and precipitated pellet were resolved on an agarose DNA gel to check the digestion pattern across replicates and samples. 5% of each chromatin inputs were set aside before the IP.

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


text: EUROPEAN MOLECUALR BIOLOGY LABORATORY, GENOME BIOLOGY UNIT

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET Heterozygous Knock out

characteristic: SRA accession

characteristic: Submitter Id

text: ESC 129-B13

text: house mouse

characteristic: common name

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

text: public

text: Setd5 delta-SET Heterozygous Knock out

characteristic: antibody

text: ab 7030

characteristic: antibody source

text: purified polyclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

text: Protocols : Growth Protocol: For each replicate 100 million ESCs were harvested and cross linked in 1.5 mM EGS in phosphate-buffered saline (PBS) for 1h followed by 10 min cross linking in 1.5% paraformaldehyde (PFA) in PBS at room temperature. Cross-linking solution was quenched with 125 mM Glycine for 5 min. Fixed cells were spun down and washed twice with ice cold PBS freshly supplemented with protease inhibitors.Samples were snap frozen in liquid nitrogen and stored at -80C. Chromatin was prepared by re-suspending cross linked cells in hypotonic buffer on ice, followed douncing with a tissue homogenise. Samples were spun down and nuclear pellets were re-suspended in MNase digestion buffer. MNase digestion was performed at for 5 minutes 37C. MNase enzymatic activity was quenched by adding EDTA/EGTA based quenching buffer. Digested chromatin was sonicated with 3 cycles of sonication at 4C. Samples were spun down to separate insoluble chromatin. Soluble fragmented chromatin was used as ChIP input. Both soluble input and precipitated pellet were resolved on an agarose DNA gel to check the digestion pattern across replicates and samples. 5% of each chromatin inputs were set aside before the IP. Each sample input was incubated with 70 Î¼L of Invitrogen M-280 anti-rabbit beads (Invitrogen) pre-coupled for 6h at 4C with the specific antibody. Samples were incubated overnight at 4C and the following day beads were washed four times with LB3-100 buffer followed by one wash with LB3-500 buffer, followed by four washes with RIPA-250 buffer, finally beads were quickly rinsed with 10 mM Tris/1 mM EDTA buffer.

characteristic: description

text: gene knock out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Wild Type

characteristic: IndividualGeneticCharacteristics

text: ESC 129-B13

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET Homozygous Knock out

text: ab 7030

text: purified polyclonal

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: Wild Type

characteristic: SRA accession

characteristic: Submitter Id

characteristic: antibody

text: ab 7030

text: purified polyclonal

text: ESC 129-B13

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: Wild Type

text: PolII CTD Ser5ph (4H8)

text: CST 2629

characteristic: antibody source

text: monoclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET Homozygous Knock Out

characteristic: IndividualGeneticCharacteristics

text: ESC 129-B13

text: house mouse

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

text: public

text: Setd5 delta-SET Homozygous Knock Out

characteristic: SRA accession

text: PolII CTD Ser5ph (4H8)

text: CST 2629

text: monoclonal

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: Setd5 delta-SET Heterozygous Knock Out

characteristic: Submitter Id

text: ESC 129-B13

text: house mouse

characteristic: common name

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: External Id

text: public

text: Setd5 delta-SET Heterozygous Knock Out

text: PolII CTD Ser5ph (4H8)

characteristic: antibody

text: CST 2629

characteristic: antibody source

text: monoclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

characteristic: description

text: gene knock out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Wild Type

characteristic: IndividualGeneticCharacteristics

text: Active Motif 39925

text: purified polyclonal

text: ESC 129-B13

text: house mouse

text: Protocols : Growth Protocol: For each replicate 20 million ESCs were harvested and cross linked for 10 minutes in 1% paraformaldehyde in PBS at room temperature. Cross-linking solution was quenched with 125 mM Glycine for 5 min. Fixed cells were spun down and washed twice with ice cold PBS freshly supplemented with protease inhibitors.Samples were snap frozen in liquid nitrogen and stored at -80C. Chromatin was prepared by re-suspending cross linked cells in hypotonic buffer on ice, followed douncing with a tissue homogenize. Samples were spun down and nuclear pellets were re-suspended in MNase digestion buffer. MNase digestion was performed at for 5 minutes 37C. MNase enzymatic activity was quenched by adding EDTA/EGTA based quenching buffer. Digested chromatin was sonicated with 3 cycles of sonicator at 4C.Samples were spun down to separate insoluble chromatin. Soluble fragmented chromatin was used as ChIP input. Both soluble input and precipitated pellet were resolved on an agarose DNA gel to check the digestion pattern across replicates and samples. 5% of each chromatin inputs were set aside before the IP.

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

text: public

text: Setd5 delta-SET Homozygous Knock out

characteristic: SRA accession

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Setd5 delta-SET Homozygous Knock out

characteristic: Submitter Id

characteristic: antibody

text: Active Motif 39925

text: purified polyclonal

text: ESC 129-B13

text: house mouse

characteristic: common name

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: Setd5 delta-SET Homozygous Knock out

text: Active Motif 39925

characteristic: antibody source

text: purified polyclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

text: Protocols : Growth Protocol: No protocol selected

characteristic: description

text: gene knock out

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET Heterozygous Knock out

characteristic: IndividualGeneticCharacteristics

characteristic: SRA accession

text: Active Motif 39925

text: purified polyclonal

text: ESC 129-B13

text: house mouse

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Wild Type

text: embase-sample-30379:ChIP_ChIP_H3K27ac_WT1

text: Active Motif 39133

text: purified polyclonal

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

text: public

text: Wild Type

text: embase-sample-30380:ChIP_ChIP_H3K27ac_WT2

characteristic: Submitter Id

characteristic: antibody

text: Active Motif 39133

text: purified polyclonal

text: ESC 129-B13

text: house mouse

characteristic: common name

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: INSDC center name

text: public

text: Setd5 delta-SET-Heterozygous Knock out

text: embase-sample-30381:ChIP_ChIP_H3K27ac_DSETI2

text: Active Motif 39133

characteristic: antibody source

text: purified polyclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

characteristic: description

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET-Homozygous Knock out

characteristic: IndividualGeneticCharacteristics

characteristic: SRA accession

text: embase-sample-30382:ChIP_ChIP_H3K27ac_DSETG4

text: Active Motif 39133

text: purified polyclonal

text: ESC 129-B13

text: house mouse

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Setd5 delta-SET-Heterozygous Knock out

text: embase-sample-30383:ChIP_ChIP_H3K27ac_DSETI3

text: Active Motif 39133

text: purified polyclonal

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: gene knock out

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: INSDC center name

text: public

text: Setd5 delta-SET-Heterozygous Knock out

text: embase-sample-30384:ChIP_Input_H3K27ac_DSETI2

characteristic: Submitter Id

text: ESC 129-B13

text: house mouse

characteristic: common name

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


text: public

text: Wild Type

text: embase-sample-30385:ChIP_Input_H3K27ac_WT2

text: ESC 129-B13

text: house mouse

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: Setd5 delta-SET-Homozygous Knock out

text: embase-sample-30386:ChIP_ChIP_H3K27ac_DSETG6

characteristic: antibody

text: Active Motif 39133

characteristic: antibody source

text: purified polyclonal

characteristic: antibody type

text: ESC 129-B13

text: house mouse

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Setd5 delta-SET-Homozygous Knock out

characteristic: IndividualGeneticCharacteristics

characteristic: SRA accession

text: embase-sample-30387:ChIP_Input_H3K27ac_DSETG6

text: ESC 129-B13

text: house mouse

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: Setd5 FLAG-HA Knock In

characteristic: Submitter Id

text: HA-tag (12CA5)

text: Roche 11583816001

text: monoclonal

text: ESC 129-B13

characteristic: cell line

text: house mouse

text: gene knock in

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: Wild Type

text: HA-tag (12CA5)

text: Roche 11583816001

text: monoclonal

text: ESC 129-B13

text: house mouse

characteristic: common name

characteristic: description

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: Setd5 FLAG-HA Knock In

text: embase-sample-29965:ChIP_Input_Setd5_KI2

text: ESC 129-B13

text: house mouse

text: gene knock in

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Wild Type - CRISPR Control

characteristic: IndividualGeneticCharacteristics

text: ESC 129-B13

text: Embryonic Stem Cells

characteristic: cell type

text: house mouse

text: Protocols : Growth Protocol: mESC growth: Mouse embryonic stem cells (129B-13) were cultured in ESC media containing Knockout-DMEM (Thermo Fisher) with 15% EmbryoMax FBS (Millipore) and 20 ng/ml leukemia inhibitory factor (LIF, produced by Protein Expression Facility at EMBL Heidelberg), 1% non-essential amino acids, 1% Glutamax, 1% Pen/Strep, 1% of 55mM beta-Mercaptoethanol solution. Cells were maintained at 37C with 5% CO2. mESCs were used as neuronal differentiation Day 0 (D0). Neuronal Differentiation: mESCs were differentiated into glutamatergic neurons according to Bibel et al. (Nature Protocols, 2007) with small modifications. mESCs were resuspended in differentiation media without LIF and grown in suspension using non-adherent plates to promote the formation of embryoid bodies. Differentiation media was changed every two days. On day 4 retinoic acid was added to the media. Embryoid bodies were cultured for 4 additional days in the presence of retinoic acid to obtain neural precursor cells on differentiation day 8. For neural monolayer culture, plates were pre-coated with Poly-D-Lysin and Laminin. On day 8, Embryoid bodies were dissociated with trypsin and cells were plated in N2 media (regular DMEM supplemented with 1xN2 and 1xB27-VitaminA (Thermo Fisher)) at a density of 200.000 cells/cm2 on precoated plates. N2 media was changed every two days without exposing neuron culture to oxygen. Four days after plating, neurons were harvested after a total of 12 differentiation days (D12).

text: Day zero

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: Wild Type

characteristic: SRA accession

characteristic: Submitter Id

text: ESC 129-B13

characteristic: cell line

text: Embryonic Stem Cells

text: house mouse

text: Day zero

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: Wild Type

text: ESC 129-B13

text: Embryoid Bodies

text: house mouse

characteristic: common name

text: Day four

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: Wild Type - CRISPR Control

text: ESC 129-B13

text: Embryoid Bodies

text: house mouse

characteristic: description

text: Day four

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Cassette Exchange Setd5 Heterozygous Knock out

characteristic: IndividualGeneticCharacteristics

text: ESC 129-B13

text: Neurons

characteristic: cell type

text: house mouse

text: Day twelve

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: Wild Type - CRISPR Control

characteristic: SRA accession

characteristic: Submitter Id

text: ESC 129-B13

text: Neuronal Precursor Cells

text: house mouse

text: Day eight

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: ESC 129-B13

characteristic: cell line

text: Neuronal Precursor Cells

text: house mouse

characteristic: common name

text: Day eight

text: gene knock out

text: Mus musculus

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: Wild Type

text: ESC 129-B13

text: Neurons

text: house mouse

characteristic: description

text: Day twelve

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: male

characteristic: sex


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Wild Type - CRISPR Control

characteristic: IndividualGeneticCharacteristics

text: ESC 129-B13

text: Neurons

characteristic: cell type

text: house mouse

text: Day twelve

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male

characteristic: title


characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ESC 129-B13

text: Embryoid Bodies

text: house mouse

text: Day four

text: gene knock out

characteristic: geneticmodification

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC first public

text: public

text: ESC 129-B13

characteristic: cell line

text: Embryonic Stem Cells

text: house mouse

characteristic: common name

text: Day zero

characteristic: developmental stage

text: gene knock out

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: public

text: Wild Type

text: ESC 129-B13

text: Neuronal Precursor Cells

text: house mouse

characteristic: description

text: Day eight

text: Mus musculus

characteristic: organism

text: Mus musculus

characteristic: sampletype

text: Mus musculus

text: male


text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: subject id

text: Mus musculus


text: Homo sampiens

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: title


text: Carrington's Featherwort

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: Carrington's Featherwort

text: Plagiochila carringtonii

text: Plagiochila carringtonii


text: Red Mason Bee

text: SC

text: public

text: Red Mason Bee

characteristic: common name

text: Osmia bicornis bicornis

text: Osmia bicornis bicornis


text: Oxford Ragwort

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Oxford Ragwort

text: Senecio squalidus

text: Senecio squalidus


text: Asian Hornet

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Asian Hornet

text: Vespa velutina

text: Vespa velutina


Figure 2_0-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_0-A

text: Please see associated paper - Determining the Mutation Bias of Favipiravir in Influenza Using Next-generation Sequencing

characteristic: description

text: Influenza A virus (A/Victoria/3/1975(H3N2))

text: Primer ID sequencing to determine mutation bias caused by favipiravir.


Figure 2_0-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_0-B

characteristic: organism


Figure 2_100-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_100-A


Figure 2_100-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_100-B


Figure 2_10-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_10-A


Figure 2_10-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_10-B


Figure 2_1-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_1-A


Figure 2_1-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_1-B


Figure 2_20-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_20-A


Figure 2_20-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_20-B


Figure 2_50-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_50-A


Figure 2_50-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 2_50-B


text: New Zealand Flatworm

text: SC

text: public

text: New Zealand Flatworm

text: Arthurdendyus triangulatus

text: Arthurdendyus triangulatus


Figure 3_Virus-0-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-0-A

text: Influenza A virus (A/England/195/2009(H1N1))

text: Primer ID sequencing to determine mutation bias caused by favipiravir in virus.


Figure 3_Virus-0-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-0-B


Figure 3_Virus-0-C

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-0-C


Figure 3_Virus-100-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-100-A


Figure 3_Virus-100-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-100-B


Figure 3_Virus-100-C

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-100-C


Figure 3_Virus-10-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-10-A


Figure 3_Virus-10-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-10-B


Figure 3_Virus-10-C

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-10-C


Figure 3_Virus-1-A

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-1-A


Figure 3_Virus-1-B

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-1-B


Figure 3_Virus-1-C

text: IMPERIAL COLLEGE LONDON

text: public

text: Figure 3_Virus-1-C


text: Division of Micorbiology

text: public

tag: Namespace:Division of Micorbiology

text: MGRAST

characteristic: broker name

characteristic: collection date

text: 1100 days, 0:00:00

characteristic: collection time

text: Sample2 Taxonomy ID:256318

text: terrestrial biome

characteristic: environment (biome)

text: microbial feature

characteristic: environment (feature)

text: organic material

characteristic: environment (material)

text: host-associated

characteristic: environmental package

text: India

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: IVRI, Izzatnagar, Bareilly

characteristic: geographic location (region and locality)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Molecular and Functional diversity of bacteria associated with earthworm gut

characteristic: project name

characteristic: sample name

text: metagenome

text: abi-solid

characteristic: sequencing method

text: Sample2 Taxonomy ID:256318


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Micorbiology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: 1100 days, 0:00:00

text: Sample1 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

text: microbial feature

text: organic material

text: host-associated

text: India

text: IVRI, Izzatnagar, Bareilly

text: host-associated

text: mimarks-survey

text: metagenome

characteristic: organism

text: metagenome

text: abi-solid

text: Sample1 Taxonomy ID:256318

characteristic: title


text: University of Copenhagen

text: public

tag: Namespace:University of Copenhagen

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: Fucopharm_assembly Taxonomy ID:256318

text: culturing environment

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: coastal sea water

characteristic: environment (material)

text: miscellaneous

characteristic: environmental package

text: Denmark

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Zealand

characteristic: geographic location (region and locality)

text: metagenome

characteristic: investigation type

characteristic: mgrast id

text: miscellaneous natural or artificial environment

characteristic: miscellaneous environmental package

text: metagenome

text: Enrichment culture established on brown macroalgae

text: metagenome

text: illumina

text: Fucopharm_assembly Taxonomy ID:256318


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences

characteristic: Submitter Id

text: MGRAST

text: SS_D8 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

text: organic feature

text: sludge

text: wastewater|sludge

text: China

text: Beijing

text: mimarks-survey

text: metagenome

text: Microbial community response to different substrates during anaerobic digestion

characteristic: project name

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method

text: SS_D8 Taxonomy ID:256318

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: Research Center for Eco-Environmental Sciences,Chinese Academy of Sciences

text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

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text: CM_D44 Taxonomy ID:256318

text: terrestrial biome

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text: organic feature

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text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

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text: metagenome

characteristic: organism

text: metagenome

text: illumina

text: CM_D44 Taxonomy ID:256318

characteristic: title

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

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text: public

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text: MGRAST

text: TSS_D44 Taxonomy ID:256318

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text: terrestrial biome

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text: China

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text: wastewater/sludge


text: public

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text: TSS_D20 Taxonomy ID:256318

text: terrestrial biome

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text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

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characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

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text: Beijing

characteristic: geographic location (region and locality)

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text: illumina

text: TSS_D20 Taxonomy ID:256318

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characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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text: public

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text: wastewater/sludge


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text: TPM Taxonomy ID:256318

text: terrestrial biome

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text: organic feature

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text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

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characteristic: sample name

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text: TPM Taxonomy ID:256318

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

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characteristic: INSDC center name

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text: public

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text: MGRAST

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text: China

text: Beijing

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characteristic: mgrast id

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text: SS_D0 Taxonomy ID:256318

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

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text: CM_D8 Taxonomy ID:256318

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

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text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: metagenome

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text: CM_D8 Taxonomy ID:256318

characteristic: title

text: wastewater/sludge