characteristic: External Id

text: CLM

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: saliva_microbiota_collected_from_caries_develop_subject18_at_follow_up_sampling_time

characteristic: description

text: microbiome

characteristic: environment (biome)

text: biofilm

text: saliva

text: South Korea

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: pyrosequencing

characteristic: title


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CLM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: saliva_microbiota_collected_from_caries_develop_subject19_at_follow_up_sampling_time

text: microbiome

text: biofilm

characteristic: environment (feature)

text: saliva

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: humam oral environmental package

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method

type: has member


characteristic: External Id

text: CLM

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: saliva_microbiota_collected_from_caries_develop_subject20_at_follow_up_sampling_time

characteristic: description

text: microbiome

characteristic: environment (biome)

text: biofilm

text: saliva

text: South Korea

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: pyrosequencing

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CLM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: saliva_microbiota_collected_from_caries_develop_subject21_at_follow_up_sampling_time

text: microbiome

text: biofilm

characteristic: environment (feature)

text: saliva

text: South Korea

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: pyrosequencing


text: CLM

text: public

text: saliva_microbiota_collected_from_caries_develop_subject22_at_follow_up_sampling_time

text: microbiome

text: biofilm

text: saliva

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-oral

characteristic: humam oral environmental package

text: metagenome

characteristic: investigation type

text: metagenome

characteristic: project name

text: metagenome

text: pyrosequencing

characteristic: sequencing method


characteristic: External Id

text: CLM

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: saliva_microbiota_collected_from_caries_develop_subject23_at_follow_up_sampling_time

characteristic: description

text: microbiome

characteristic: environment (biome)

text: biofilm

text: saliva

text: South Korea

text: human-oral

text: metagenome

text: metagenome

characteristic: organism

text: metagenome

text: pyrosequencing

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CLM

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: collection date

text: saliva_microbiota_collected_from_caries_develop_subject24_at_follow_up_sampling_time

text: microbiome

text: biofilm

characteristic: environment (feature)

text: saliva

text: South Korea

text: human-oral

text: metagenome

text: metagenome

text: metagenome

text: pyrosequencing


text: INRA (INRA Toulouse)

text: public

tag: Namespace:INRA (INRA Toulouse)

text: tomato

characteristic: common name

text: micro.Tom

characteristic: cultivar

characteristic: dev stage

text: Solanum lycopersicum

text: Solanum lycopersicum

text: ovary

characteristic: tissue type

text: samples corresponding to fruit set process in tomato


characteristic: External Id

text: INRA (INRA Toulouse)

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: tomato

text: micro.Tom

text: Solanum lycopersicum

text: Solanum lycopersicum


E-MTAB-5519:Sample 1

text: University of Cambridge

text: public

text: E-MTAB-5519:Sample 1

tag: Namespace:University of Cambridge

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: human

text: Protocols: For Ribo-Seq, parental HEK293 and PDE12-/- cells were treated with 100 μg/ml chloramphenicol and 100 μg/mL cycloheximide for 5 min. Cells were rinsed with 5 ml of ice-cold PBS, the dishes were submerged in a reservoir of liquid nitrogen for 10 s and transferred to dry ice. Cells were lysed in 400 μl of lysis buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1 % Triton X-100, 100 μg/ml chloramphenicol and cycloheximide). Cells were scraped and lysates clarified by centrifugation for 20 min at 13,000 g at 4°C. 200 μl aliquots of cell lysates were treated with 7.5 μl RNase 1 (100 units/μl) at 28°C. The reaction was layered onto a 10-30 % sucrose gradient [2ml 10-30% (v/v)] in 50mM Tris-HCl (pH7.2), 20mM Mg(OAc)2, 80mM NH4Cl, 0.1M KCl, 1mM PMSF and centrifuged for 2h 15min at 100,000 gmax at 4°C (39,000 rpm, Beckman Coulter TLS-55 rotor) and fractions collected. Subsequently, all fractions containing mitochondrial monosomes, ascertained by western blotting, were pooled and digested with proteinase K (200 μg/ml) for 30 min at 42°C. RPFs were recovered by extracting twice with pre-warmed (65°C) acidic phenol:chloroform and once with chloroform (1:1, v/v, buffered with 10 mM Tris pH 7.5, 0.1 mM EDTA) followed by ethanol precipitation. RPFs (1 μg) were separated on 15 % denaturing polyacrylamide gels and RNA species migrating between 25 and 35 nt were harvested. RNA was eluted from the gel slices and ethanol precipitated. The RNA samples from above were heated at 80°C for 2 min, cooled and the 3’ phosphate group removed using T4 polynucleotide kinase (New England Biolabs) for 2 h at 37°C in a 20 μl reaction. The RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated in a 20 μl reaction overnight at 14°C to a preadenylated 3’-adaptor using T4 RNA Ligase 2 (New England Biolabs). RNA was precipitated, loaded into a 15 % denaturing polyacrylamide gel and ligated RNA fragments migrating between 48 and 54 nt were excised. The RNA was eluted, precipitated, resuspended as above, and 5’ phosphorylated using T4 PNK in the presence of 1 mM ATP for 2 h at 37°C. RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated to a 5’ RNA adaptor overnight at 14°C using T4 RNA Ligase (New England Biolabs). The fully adapted RNAs were recovered by ethanol precipitation, dissolved in 6 μl 10 mM Tris-HCl (pH 7.5), and ligated product annealed to an RT primer for 5 min at 65°C. The RNA was subsequently reverse transcribed for 50 min at 55°C in using SuperScript III according to manufacturer’s instructions, followed by heat inactivation for 5 min at 85°C. Standard PCR reactions were used to prepare amplicons using forward primer RP1 and RPIX as reverse primer, where X is primer number (1-24). PCR reactions were loaded onto 10 % non-denaturing polyacrylamide-TBE gels and products of ~150 bp were excised from the gel and eluted. These amplicon libraries were ethanol precipitated and resuspended in 15 μl 10 mM Tris-HCl (pH 7.5). Ribosomal RNA was depleted from Ribo-seq samples at the library amplicon stage; 12 µL of the relevant Ribo-seq library was mixed with 4 µL of 4× hybridization buffer (200 mM HEPES pH 7.5 and 2 M NaCl) and denatured at 98°C for 2 min. DNA was re-annealed for 5 h at 68°C prior to addition of 2 µL of 10× DSN master buffer and 2 µL of DSN (4 units, Evrogen). Digestion was allowed to proceed for 25 min at 68°C, before addition of 20 µL 10 mM EDTA and incubation for a further 5 min at 68°C. DNA was recovered by a single extraction with phenol-chloroform (1:1, vol/vol) followed by ethanol precipitation and resuspended in 4 µL 10 mM Tris-HCl pH 7.5. The treated amplicon library was subjected to another round of PCR (as above) and the resulting library subjected to a second round of DSN treatment.

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Homo sapiens

text: Sample 1

characteristic: title


E-MTAB-5519:Sample 2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University of Cambridge

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5519:Sample 2

text: ArrayExpress

text: HEK293 PDE12-/-

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 2


E-MTAB-5519:Sample 3

text: University of Cambridge

characteristic: INSDC last update

text: public

text: E-MTAB-5519:Sample 3

text: ArrayExpress

text: deltaFLP 143B cybrid

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens

text: Sample 3


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition A - replicate 1

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition A - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition A - replicate 3

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition A - replicate 1

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition A - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition A - replicate 3

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition B - replicate 1

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition B - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition B - replicate 3

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition B - replicate 1

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition B - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition B - replicate 4

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition D - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition D - replicate 3

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 56 (latitude) - light condition D - replicate 4

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition D - replicate 1

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition D - replicate 2

text: Pinus sylvestris

text: Pinus sylvestris


text: UPSC

text: public

text: Scots pine

text: Pine ecotype 67 (latitude) - light condition D - replicate 3

text: Pinus sylvestris

text: Pinus sylvestris


Cow Rumen

text: gozbayram

text: public

text: Cow Rumen

text: Cow Rumen

text: uncultured bacterium

text: uncultured bacterium

text: Cow Rumen


Goat Rumen

text: gozbayram

text: public

text: Goat Rumen

text: Goat Rumen

text: uncultured bacterium

text: uncultured bacterium

text: Goat Rumen


Cow Rumen Enrichment

text: gozbayram

text: public

text: Cow Rumen Enrichment

text: Cow Rumen Enrichment

text: uncultured bacterium

text: uncultured bacterium

text: Cow Rumen Enrichment


Goat Rumen Enrichment

text: gozbayram

text: public

text: Goat Rumen Enrichment

text: Goat Rumen Enrichment

text: uncultured bacterium

text: uncultured bacterium

text: Goat Rumen Enrichment


Sorghum Reactor

text: gozbayram

text: public

text: Sorghum Reactor

text: Sorghum Reactor

text: uncultured bacterium

text: uncultured bacterium

text: Sorghum Reactor


Sorghum Enrichment

text: gozbayram

text: public

text: Sorghum Enrichment

text: Sorghum Enrichment

text: uncultured bacterium

text: uncultured bacterium

text: Sorghum Enrichment


text: University Hospital Galway

text: public

tag: Namespace:University Hospital Galway

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Shigella sonnei

text: Shigella sonnei


characteristic: External Id

text: University Hospital Galway

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

text: Shigella dysenteriae

text: Shigella dysenteriae


text: public

tag: Namespace:UNIVERSITY OF SHEFFIELD, DEPARTMENT OF ANIMAL & PL

text: closed circuit

characteristic: description

text: No

characteristic: environmental sample

text: electrode

text: metagenome

characteristic: organism

text: metagenome

text: FuelCell

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF SHEFFIELD, DEPARTMENT OF ANIMAL & PL

characteristic: INSDC center name

text: public

text: closed circuit

text: No

text: electrode

text: metagenome

text: metagenome

text: FuelCell


characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: open circuit

text: No

text: electrode

text: metagenome

text: metagenome

text: FuelCell


text: public

text: Open circuit

text: No

text: electrode

text: metagenome

text: metagenome

text: FuelCell


text: UPSC

text: public

text: Norway spruce

characteristic: common name

text: Spruce ecotype 56 (latitude) - light condition A - replicate 2

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition A - replicate 4

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition A - replicate 5

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition A - replicate 1

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition A - replicate 3

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition A - replicate 4

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition B - replicate 4

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition B - replicate 5

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition B - replicate 6

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition B - replicate 2

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition B - replicate 3

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition B - replicate 4

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition D - replicate 1

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition D - replicate 2

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 56 (latitude) - light condition D - replicate 3

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition D - replicate 1

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition D - replicate 2

text: Picea abies

text: Picea abies


text: UPSC

text: public

text: Norway spruce

text: Spruce ecotype 67 (latitude) - light condition D - replicate 4

text: Picea abies

text: Picea abies


text: Pseudomonas aeruginosa

characteristic: ArrayExpress-Species

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


text: public

tag: Namespace:Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences

text: taimen

text: A pooled total RNA sample of 12 tissues dissected from one individuals at age 4+

text: Hucho taimen

text: Hucho taimen

text: RNA-Seq samples of Hucho taimen


text: Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences

text: public

text: taimen

text: A pooled total RNA sample of 12 tissues dissected from 9 individual at age 1 to 4

text: Hucho taimen

text: Hucho taimen

text: RNA-Seq samples of Hucho taimen


text: the Netherlands Institute of Ecology

text: public

tag: Namespace:the Netherlands Institute of Ecology

characteristic: collection date

text: Black Water

text: Netherlands

characteristic: geographic location (country and/or sea)

text: metagenome

characteristic: investigation type

characteristic: name of the sampling site

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

characteristic: sewage type

text: Black Water Project


characteristic: External Id

text: the Netherlands Institute of Ecology

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Sludge UASB

characteristic: description

text: Netherlands

text: metagenome

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

text: Black Water Project


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: the Netherlands Institute of Ecology

text: public

text: Effluent UASB

text: Netherlands

text: metagenome

text: wastewater metagenome

characteristic: organism

text: wastewater metagenome

text: wastewater treatment plant

text: Black Water Project

characteristic: title


characteristic: ENA-LAST-UPDATE

text: the Netherlands Institute of Ecology

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Effluent PBR

text: Netherlands

text: metagenome

text: wastewater metagenome

text: wastewater metagenome

text: wastewater treatment plant

text: Black Water Project


text: Homo sapiens

characteristic: ArrayExpress-Species

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens


text: Genoscope CEA

text: public

tag: Namespace:Genoscope CEA

text: Acidithiobacillus ferrivorans CF27

text: Acidithiobacillus ferrivorans

text: Acidithiobacillus ferrivorans

text: Prokaryotic genome sequencing


text: public

tag: Namespace:Institute of Microbiology and Infection School of Biosciences University of Birmingham

text: ArrayExpress

characteristic: broker name

text: Protocols: Prototypical enterotoxigenic Escherichia coli strain first isolated from a patient with cholera-like symptoms in Bangladesh prior to 1973 Cells were grown in liquid LB medium at 37 degrees with shaking Immunoprecipitations were done as described by Haycocks et al. (PLoS Pathog. 2015. 11:e1004605) using bacterial strain H10407 transformed with plasmid pRGM9818 encoding marA under the control of the tac promoter. This allowed us to circumvent repression of the chromosomal mar locus by MarR. After growing cells to midlog phase, crosslinking, and sonication, protein DNA complexes were immunoprecipitated using anti-sigma70, anti-MarA or anti-MarR. Anti-sigma70 was purchased from Neoclone (Madison, USA). Anti-MarA and anti-MarR were a kind gift from Lee Rosner and Bob Martin (NIH, Bethesda). Libraries were prepared using immunoprecipited protein-DNA complexes immobilised with Protein A-sepharose. DNA fragments were then blunt ended, A-tailed and barcoded. This was done using an NEB quick blunting and ligation kit, the Klenow fragment (5’-3’ exo-, NEB) and NEXTflex ChIP-seq barcodes (Bioo Scientific). Following elution of complexes from the Protein-A sepharose, crosslinks were reversed and barcoded libraries were amplified by PCR. The number of PCR cycles was determined empirically for each library. After amplification, library concentration was quantified using Qubit analysis and real time PCR.

text: transformed with plasmid pRGM9818

characteristic: genotype

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli

characteristic: strain


characteristic: External Id

text: Institute of Microbiology and Infection School of Biosciences University of Birmingham

text: public

characteristic: INSDC status

text: ArrayExpress

text: transformed with plasmid pRGM9818

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: EMBL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Mus musculus


text: Vibrio cholerae

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Vibrio cholerae

text: Vibrio cholerae

text: Vibrio cholerae


characteristic: ENA-FIRST-PUBLIC

text: public

tag: Namespace:School of Computing Science, Newcastle University

characteristic: collection date

text: Seawater

characteristic: environment (biome)

text: Seawater

characteristic: environment (feature)

text: Water

characteristic: environment (material)

text: North Sea

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: metagenome

text: NUFEB Collaborations

characteristic: project name

text: metagenome

text: Illumina MiSeq

characteristic: sequencing method

text: North Sea - 2S - t0

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: School of Computing Science, Newcastle University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Seawater

text: Seawater

text: Water

text: North Sea

text: metagenome

text: metagenome

characteristic: organism

text: NUFEB Collaborations

text: metagenome

text: Illumina MiSeq

text: North Sea - 1N - t0

characteristic: title

text: water


E-MTAB-5527:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

text: E-MTAB-5527:Sample 1

tag: Namespace:Wellcome Trust Sanger Institute

characteristic: Submitter Id

text: frozen sample

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Human polyA+ RNAs were purchased from Clontech. According to the manufacturer, normal organ samples were pooled from a variable number of deceased individuals who had died of sudden death at a wide range of ages. RNA was isolated from these samples using a modified guanidium thiocynate extraction method, and enriched in polyA+ RNAs with two rounds of oligo(dT)-cellulose column purification. First-strand cDNA samples were prepared from human poly(A)+ RNAs (BD-Clontech) with the SuperScript III kit (Invitrogen). Amplifications were performed in a final volume of 12.5 Î¼L with JumpStart REDTaq ReadyMix (Sigma-Aldrich) and a primer concentration of 0.4 Î¼M in 384-well plates format on an automatized Evoware platform (TECAN) combined with a Tetrad2 thermocycler (Bio-Rad) that allows processing four plates in parallel. Because monoexonic amplification is sensitive to genomic DNA contaminations, monoexonic models were assessed by amplification of cDNA in which a dNTP analog was incorporated using the mRNA Selective PCR Kit (TAKARA).

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 1


E-MTAB-5527:Sample 10

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 10

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: pancreas

text: Homo sapiens

text: mixed sex

text: Sample 10


E-MTAB-5527:Sample 11

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5527:Sample 11

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: small intestine

text: Homo sapiens

text: mixed sex

text: Sample 11


E-MTAB-5527:Sample 12

text: Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5527:Sample 12

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: spleen

text: Homo sapiens

text: mixed sex

text: Sample 12


E-MTAB-5527:Sample 13

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 13

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: testis

text: Homo sapiens

text: male

text: Sample 13

characteristic: title


E-MTAB-5527:Sample 14

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 14

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: thymus

text: Homo sapiens

text: mixed sex

text: Sample 14


E-MTAB-5527:Sample 15

text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

text: E-MTAB-5527:Sample 15

characteristic: Submitter Id

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: mixed sex

text: Sample 15


E-MTAB-5527:Sample 16

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 16

text: frozen sample

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: tonsil

text: Homo sapiens

text: mixed sex

text: Sample 16


E-MTAB-5527:Sample 17

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 17

text: frozen sample

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: male

text: Sample 17


E-MTAB-5527:Sample 18

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 18

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: fetus

characteristic: organism part

text: Homo sapiens

text: mixed sex

characteristic: sex

text: Sample 18


E-MTAB-5527:Sample 19

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 19

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: Sample 19


E-MTAB-5527:Sample 2

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5527:Sample 2

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: fetus

text: Homo sapiens

text: mixed sex

text: Sample 2


E-MTAB-5527:Sample 20

text: Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5527:Sample 20

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: mixed sex

text: Sample 20


E-MTAB-5527:Sample 21

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 21

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: liver

text: Homo sapiens

text: male

text: Sample 21

characteristic: title


E-MTAB-5527:Sample 22

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 22

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: mixed sex

text: Sample 22


E-MTAB-5527:Sample 23

text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

text: E-MTAB-5527:Sample 23

characteristic: Submitter Id

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: mixed sex

text: Sample 23


E-MTAB-5527:Sample 24

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 24

text: frozen sample

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: female

text: Sample 24


E-MTAB-5527:Sample 25

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 25

text: frozen sample

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: muscle

text: Homo sapiens

text: male

text: Sample 25


E-MTAB-5527:Sample 26

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 26

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: pancreas

characteristic: organism part

text: Homo sapiens

text: mixed sex

characteristic: sex

text: Sample 26


E-MTAB-5527:Sample 27

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 27

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: small intestine

text: Homo sapiens

text: mixed sex

text: Sample 27


E-MTAB-5527:Sample 28

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5527:Sample 28

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: spleen

text: Homo sapiens

text: mixed sex

text: Sample 28


E-MTAB-5527:Sample 29

text: Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5527:Sample 29

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: testis

text: Homo sapiens

text: male

text: Sample 29


E-MTAB-5527:Sample 3

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 3

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: heart

text: Homo sapiens

text: male

text: Sample 3

characteristic: title


E-MTAB-5527:Sample 30

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 30

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: thymus

text: Homo sapiens

text: mixed sex

text: Sample 30


E-MTAB-5527:Sample 31

text: Wellcome Trust Sanger Institute

text: public

characteristic: SRA accession

text: E-MTAB-5527:Sample 31

characteristic: Submitter Id

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: thyroid gland

text: Homo sapiens

text: mixed sex

text: Sample 31


E-MTAB-5527:Sample 32

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 32

text: frozen sample

characteristic: biosource type

text: ArrayExpress

characteristic: broker name

text: human

text: Homo sapiens

text: Homo sapiens

text: tonsil

text: Homo sapiens

text: mixed sex

text: Sample 32


E-MTAB-5527:Sample 4

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 4

text: frozen sample

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

text: mixed sex

text: Sample 4


E-MTAB-5527:Sample 5

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 5

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex

text: Sample 5


E-MTAB-5527:Sample 6

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 6

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: lung

text: Homo sapiens

text: mixed sex

text: Sample 6


E-MTAB-5527:Sample 7

text: Wellcome Trust Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-5527:Sample 7

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: lymph node

text: Homo sapiens

text: mixed sex

text: Sample 7


E-MTAB-5527:Sample 8

text: Wellcome Trust Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5527:Sample 8

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: mammary gland

text: Homo sapiens

text: female

text: Sample 8


E-MTAB-5527:Sample 9

text: Wellcome Trust Sanger Institute

text: public

text: E-MTAB-5527:Sample 9

text: frozen sample

text: ArrayExpress

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: muscle

text: Homo sapiens

text: male

text: Sample 9

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF WESTERN ONTARIO

text: public

tag: Namespace:UNIVERSITY OF WESTERN ONTARIO

text: Illumina forward: ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT; illumina reverse: CGG TCT CGG CAT TCC TGC TGA ACC GCT CTT CCG ATC T

characteristic: adapters

characteristic: collection date

text: July Komoka uninvaded

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

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: AMV4.5N_7F CCAAGGCC AMDG_9R AGCCACAC

characteristic: multiplex identifiers

characteristic: nucleic acid amplification

characteristic: nucleic acid extraction

text: fungus metagenome

text: 94°C for 1 min, 29 cycles of 94°C for 30 s, 55°C for 30 s, 72°C for 18 s. No final extension step was used.

characteristic: pcr conditions

characteristic: pcr primers

characteristic: project name

unit: g

characteristic: sample weight for DNA extraction

text: fungus metagenome

text: Illumina Miseq 2x300 bp

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: frozen

characteristic: storage conditions (fresh/frozen/other)

text: nuclear ribosomal DNA gene, small subunit

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: July Komoka invaded

characteristic: description

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

text: metagenome

text: AMV4.5N_7F CCAAGGCC AMDG_10R CAGGCTTA

text: fungus metagenome

characteristic: organism

text: fungus metagenome

text: Illumina Miseq 2x300 bp

text: soil

text: frozen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF WESTERN ONTARIO

text: public

text: October Komoka invaded

text: Temperate hardwood forest

text: riparian zone; sugar maple stand

text: soil

text: Canada

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: AMV4.5N_7F CCAAGGCC AMDG_16R TCCGCCAA

characteristic: multiplex identifiers

characteristic: nucleic acid amplification

characteristic: nucleic acid extraction

text: fungus metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: project name

characteristic: sample weight for DNA extraction

text: fungus metagenome

text: Illumina Miseq 2x300 bp

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: frozen

characteristic: storage conditions (fresh/frozen/other)

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: June Cliffs invaded

characteristic: description

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

text: metagenome

text: AMV4.5N_7F CCAAGGCC AMDG_8R TGACTTCA

text: fungus metagenome

characteristic: organism

text: fungus metagenome

text: Illumina Miseq 2x300 bp

text: soil

text: frozen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF WESTERN ONTARIO

text: public

text: October Cliffs uninvaded

text: Temperate hardwood forest

text: riparian zone; sugar maple stand

text: soil

text: Canada

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: AMV4.5N_7F CCAAGGCC AMDG_13R GCTTGATG

characteristic: multiplex identifiers

characteristic: nucleic acid amplification

characteristic: nucleic acid extraction

text: fungus metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: project name

characteristic: sample weight for DNA extraction

text: fungus metagenome

text: Illumina Miseq 2x300 bp

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: frozen

characteristic: storage conditions (fresh/frozen/other)

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: October Cliffs invaded

characteristic: description

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

text: metagenome

text: AMV4.5N_7F CCAAGGCC AMDG_14R TGGCGGCT

text: fungus metagenome

characteristic: organism

text: fungus metagenome

text: Illumina Miseq 2x300 bp

text: soil

text: frozen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF WESTERN ONTARIO

text: public

text: June Cliffs uninvaded

text: Temperate hardwood forest

text: riparian zone; sugar maple stand

text: soil

text: Canada

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: AMV4.5N_7F CCAAGGCC AMDG_5R AGTTAACC

characteristic: multiplex identifiers

characteristic: nucleic acid amplification

characteristic: nucleic acid extraction

text: fungus metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: project name

characteristic: sample weight for DNA extraction

text: fungus metagenome

text: Illumina Miseq 2x300 bp

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: frozen

characteristic: storage conditions (fresh/frozen/other)

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: June Cliffs invaded

characteristic: description

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

text: metagenome

text: AMV4.5N_7F CCAAGGCC AMDG_6R CCAAGGCC

text: fungus metagenome

characteristic: organism

text: fungus metagenome

text: Illumina Miseq 2x300 bp

text: soil

text: frozen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF WESTERN ONTARIO

text: public

text: October Cliffs uninvaded

text: Temperate hardwood forest

text: riparian zone; sugar maple stand

text: soil

text: Canada

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: AMV4.5N_7F CCAAGGCC AMDG_11R CTTCCTGG

characteristic: multiplex identifiers

characteristic: nucleic acid amplification

characteristic: nucleic acid extraction

text: fungus metagenome

characteristic: pcr conditions

characteristic: pcr primers

characteristic: project name

characteristic: sample weight for DNA extraction

text: fungus metagenome

text: Illumina Miseq 2x300 bp

characteristic: sequencing method

text: soil

characteristic: soil environmental package

text: frozen

characteristic: storage conditions (fresh/frozen/other)

characteristic: target gene


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF WESTERN ONTARIO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: adapters

characteristic: collection date

text: October Cliffs invaded

characteristic: description

text: Temperate hardwood forest

characteristic: environment (biome)

text: riparian zone; sugar maple stand

characteristic: environment (feature)

text: soil

characteristic: environment (material)

text: Canada

characteristic: geographic location (country and/or sea)

text: metagenome

text: AMV4.5N_7F CCAAGGCC AMDG_12R GACTAATC

text: fungus metagenome

characteristic: organism

text: fungus metagenome

text: Illumina Miseq 2x300 bp

text: soil

text: frozen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UNIVERSITY OF VIENNA

text: public

tag: Namespace:UNIVERSITY OF VIENNA

text: Nitrostalea enriched in anaerobic sulfate amendment microcosm

text: Nitrosotalea sp. SbT1

text: Nitrosotalea sp. SbT1

text: Nitrosotalea sp. SbT1


characteristic: External Id

text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Ireland

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Java

text: Java

characteristic: serovar

text: Subsp. I

characteristic: sub species


text: University Hospital Galway

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhimurium var. monophasic 4,[5],12:i:-

text: Subsp. I


text: University Hospital Galway

text: public

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Manhattan

characteristic: organism

text: Manhattan

text: Subsp. I

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhimurium

text: Typhimurium

text: Subsp. I


characteristic: External Id

text: University Hospital Galway

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar London

text: London

text: Subsp. I


text: University Hospital Galway

text: public

text: Ireland

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Infantis

text: Infantis

text: Subsp. I


text: University Hospital Galway

characteristic: INSDC last update

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Bredeney

text: Bredeney

characteristic: serovar

text: Subsp. I

characteristic: sub species


text: University Hospital Galway

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Enteritidis

text: Enteritidis

text: Subsp. I


text: Plasmodium falciparum

characteristic: ArrayExpress-Species

text: SC

text: public

text: malaria parasite P. falciparum

characteristic: common name

text: Plasmodium falciparum

characteristic: organism

text: Plasmodium falciparum


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Garvan Institute of Medical Research

text: public

tag: Namespace:Garvan Institute of Medical Research

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: osteocyte

characteristic: cell type

text: house mouse

text: Protocols: Mice were sacrificed by CO2 asphyxiation and cervical dislocation. The tibiae, femora and humeri were isolated by disarticulation from 8 mice (a total of 32 bone samples). Soft tissue including muscle, ligaments and tendons were removed, before the surface was gently scraped with a scalpel to remove the periosteum. Diaphyseal bone from the tibia was isolated by cutting the tibia at the fibulae junction and 1mm distal to the proximal growth plate, and from the femur by cutting the bone immediately proximal to the third trochanter and 1mm proximal to the distal growth plate. The humeri were cut immediately proximal to the deltoid tuberosity and then 1mm proximal to the epicondyles before completely removing the deltoid tuberosity along the bone shaft. Bone marrow from each bone was removed by first flushing with PBS until visibly clean and then centrifuging at 14,000rcf for 15 seconds. Bones from the left side were cut into pieces and snap frozen in liquid N2 prior to homogenisation and RNA extraction. Calvaria samples were collected by isolating the parietal region of the skull, excluding the sutures and gently scraping soft tissue from the bone surface. Calvaria were separated into left and right bone fragments. Bone samples were cut into 1mm strips and vortexed in a 1.5mL centrifuge tube with 200µL of PBS and then centrifuged at 14,000rcf for 15 seconds to remove bone marrow. Bones from the left side were snap frozen in liquid N2 prior to homogenisation and RNA extraction. Both samples were snap frozen for RNA isolation. All samples from each mouse were processed and snap frozen in liquid N2 within ~16 minutes of sacrifice. TRIreagent (Sigma T9424) was added directly to the frozen bone samples and homogenised using a Polytron hand held homogeniser (Kinematica PT 1200 E 11010026). RNA was isolated according to the manufacturers protocol and cleaned with an additional ethanol-precipitation step. RNA yield was determined using a Nanodrop (Thermo) and RNA integrity determined using the Bioanalyser RNA 6000 Nano Kit (Agilent Technologies 5067-1511). Total-RNA (250ng) was depleted of ribosomal RNA using RNaseH (Epicentre H39500) and ribosomal RNA targeting oligonucleotides based on a protocol by Adiconis et al., 2013 (Adiconis et al., 2013). Briefly, total RNA, spiked with ERCC internal controls (Life Technologies 4456739), was incubated with ribosomal-RNA targeting oligos and RNaseH to degrade the rRNAs before the oligos were removed with a DNase treatment (Life Technologies AM2238). RNA was repurified using magnetic beads according to the manufacturers protocol (Beckman Coulter Genomics A63987). Total-RNA, 125bp paired-end, stranded transcriptome libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit starting from the fragmentation step in the manufacturers protocol (Illumina RS-122-2201).

characteristic: description

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: cranium

characteristic: organism part

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Garvan Institute of Medical Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: osteocyte

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: femur

text: Mus musculus

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Garvan Institute of Medical Research

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: osteocyte

text: house mouse

characteristic: common name

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: humerus

text: Mus musculus

text: male


text: Garvan Institute of Medical Research

text: public

text: ArrayExpress

characteristic: broker name

text: osteocyte

characteristic: cell type

text: house mouse

characteristic: description

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: tibia

characteristic: organism part

text: Mus musculus

text: male


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Garvan Institute of Medical Research

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

text: Protocols: Mice were sacrificed by CO2 asphyxiation and cervical dislocation. Both humeri were isolated by disarticulation from 5 mice (a total of 10 bone samples). Soft tissue including muscle, ligaments and tendons were removed, before the surface was gently scraped with a scalpel to remove the periosteum. Diaphyseal bone from the humeri was isolated by cutting immediately proximal to the deltoid tuberosity and then 1mm proximal to the epicondyles before completely removing the deltoid tuberosity along the bone shaft. Bone marrow was removed from the left humeri by first flushing with PBS until visibly clean and then centrifuging at 14,000rcf for 15 seconds(\Clean_bone\ samples), whilst the marrow was retained in right humeri (\Bone_and_marrow\ samples). Bones were cut into pieces and snap frozen in liquid N2 prior to homogenisation and RNA extraction. All samples from each mouse were processed and snap frozen in liquid N2 within ~16 minutes of sacrifice. TRIreagent (Sigma T9424) was added directly to the frozen bone samples and homogenised using a Polytron hand held homogeniser (Kinematica PT 1200 E 11010026). RNA was isolated according to the manufacturers protocol and cleaned with an additional ethanol-precipitation step. RNA yield was determined using a Nanodrop (Thermo) and RNA integrity determined using the Bioanalyser RNA 6000 Nano Kit (Agilent Technologies 5067-1511). Total-RNA (250ng) was depleted of ribosomal RNA using RNaseH (Epicentre H39500) and ribosomal RNA targeting oligonucleotides based on a protocol by Adiconis et al., 2013 (Adiconis et al., 2013). Briefly, total RNA, spiked with ERCC internal controls (Life Technologies 4456739), was incubated with ribosomal-RNA targeting oligos and RNaseH to degrade the rRNAs before the oligos were removed with a DNase treatment (Life Technologies AM2238). RNA was repurified using magnetic beads according to the manufacturers protocol (Beckman Coulter Genomics A63987). Total-RNA, 125bp paired-end, stranded transcriptome libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit starting from the fragmentation step in the manufacturers protocol (Illumina RS-122-2201).

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: humerus

text: bone

characteristic: sampling site

text: Mus musculus

text: male

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Garvan Institute of Medical Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: humerus

text: bone and bone marrow

text: Mus musculus

text: male


text: Helicobacter pametensis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Helicobacter pametensis

characteristic: common name

text: Helicobacter pametensis

characteristic: organism

text: Helicobacter pametensis


text: Streptomyces gibsonii

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: Streptomyces gibsonii

text: Streptomyces gibsonii

text: Streptomyces gibsonii


text: Neisseria pharyngis

text: SC

characteristic: INSDC center name

text: public

text: Neisseria pharyngis

text: Neisseria pharyngis

text: Neisseria pharyngis


text: Legionella micdadei

text: SC

text: public

text: Legionella micdadei

text: Tatlockia micdadei

text: Tatlockia micdadei


text: University Hospital Galway

text: public

characteristic: collection date

text: Ireland

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Human

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Virchow

text: Virchow

characteristic: serovar

text: Subsp. I

characteristic: sub species


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: University Hospital Galway

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Ireland

text: Homo sapiens

text: Human

text: Salmonella enterica subsp. enterica serovar Typhi

text: Typhi

text: Subsp. I

characteristic: title


text: University Hospital Galway

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Ireland

text: Homo sapiens

text: Human

characteristic: organism

text: Subsp. I


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University Hospital Galway

characteristic: INSDC center name

text: public

text: Ireland

text: Homo sapiens

text: Human

text: Java

text: Subsp. I


characteristic: ArrayExpress-Species

text: SC

text: public

text: KEN

characteristic: common name

text: Salmonella

characteristic: genus

text: Homo sapiens

characteristic: host

type: AMR curated data - CABBAGE

value: nalidixic acid

value: CLSI

value: disk diffusion

value: mm

value: susceptible

value: Salmonella enterica

value: tetracycline

value: cefotaxime

value: ciprofloxacin

value: chloramphenicol

value: ampicillin

value: cefpodoxime

value: ceftazidime

value: ceftriaxone

value: trimethoprim-sulfamethoxazole


text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

characteristic: isolate

value: resistant

value: intermediate


characteristic: ENA-CHECKLIST

text: SC

text: public


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: nalidixic acid


text: SC

characteristic: INSDC first public

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: CLSI


text: SC

characteristic: INSDC last update

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: disk diffusion


text: SC

text: public

characteristic: INSDC status

text: KEN

text: Salmonella

text: Homo sapiens

value: mm


text: SC

text: public

characteristic: title


text: SC

text: public

text: KEN

characteristic: SRA accession

text: Salmonella

text: Homo sapiens

value: susceptible


text: SC

text: public

text: KEN

characteristic: Submitter Id

text: Salmonella

text: Homo sapiens

value: Salmonella enterica


text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

characteristic: organism

value: tetracycline


characteristic: ENA-LAST-UPDATE

text: SC

text: public


characteristic: External Id

text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: cefotaxime


text: SC

characteristic: INSDC center name

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: ciprofloxacin


characteristic: ArrayExpress-Species

text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: chloramphenicol


text: SC

text: public

text: KEN

characteristic: common name

text: Salmonella

text: Homo sapiens

value: ampicillin


text: SC

text: public

text: KEN

text: Salmonella

characteristic: genus

text: Homo sapiens

value: cefpodoxime


text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

characteristic: host

value: ceftazidime


text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

characteristic: isolate

value: ceftriaxone


characteristic: ENA-CHECKLIST

text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: trimethoprim-sulfamethoxazole


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

value: resistant


text: Salmonella enterica subsp. enterica serovar Paratyphi A

text: SC

characteristic: INSDC first public

text: public


text: SC

characteristic: INSDC last update

text: public

text: KEN

text: Salmonella

text: Homo sapiens


text: SC

text: public

characteristic: INSDC status

text: KEN

text: Salmonella

text: Homo sapiens

value: intermediate


text: Salmonella enterica subsp. enterica serovar Paratyphi C

text: SC

text: public

characteristic: title


text: Salmonella enterica subsp. enterica serovar Paratyphi B

text: SC

text: public

characteristic: SRA accession


text: SC

text: public

text: KEN

characteristic: Submitter Id

text: Salmonella

text: Homo sapiens

value: nalidixic acid


text: SC

text: public

text: KEN

text: Salmonella

text: Homo sapiens

characteristic: organism

value: CLSI


characteristic: ENA-LAST-UPDATE

text: MBL

text: public

characteristic: collection date

text: Diffuse fluid metagenome from Marker 33 vent taken in 2015

characteristic: description

text: marine

characteristic: environment (biome)

text: hydrothemal vent

characteristic: environment (feature)

text: diffuse fluid

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hydrothermal vent metagenome

text: Axial Omics 2015

characteristic: project name

text: hydrothermal vent metagenome

text: Illumina Next-Seq paired end reads with 30 bp overlap

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: MBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Diffuse fluid metatranscriptome from Marker 33 vent taken in 2015

text: marine

text: hydrothemal vent

text: diffuse fluid

text: Pacific Ocean

text: metatranscriptome

text: hydrothermal vent metagenome

text: Axial Omics 2015

text: hydrothermal vent metagenome

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

text: MBL

text: public

characteristic: Submitter Id

characteristic: collection date

text: Diffuse fluid metagenome from Anemone vent taken in 2015

characteristic: description

text: marine

characteristic: environment (biome)

text: hydrothemal vent

characteristic: environment (feature)

text: diffuse fluid

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: hydrothermal vent metagenome

characteristic: organism

text: Axial Omics 2015

text: hydrothermal vent metagenome

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MBL

text: public

text: Diffuse fluid metatranscriptome from Anemone vent taken in 2015

text: marine

text: hydrothemal vent

text: diffuse fluid

text: Pacific Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metatranscriptome

characteristic: investigation type

text: hydrothermal vent metagenome

text: Axial Omics 2015

characteristic: project name

text: hydrothermal vent metagenome

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Diffuse fluid metagenome from Marker 113 vent taken in 2015

text: marine

text: hydrothemal vent

text: diffuse fluid

text: Pacific Ocean

text: metagenome

text: hydrothermal vent metagenome

text: Axial Omics 2015

text: hydrothermal vent metagenome

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MBL

text: public

characteristic: collection date

text: Diffuse fluid metatranscriptome from Marker 113 vent taken in 2015

characteristic: description

text: marine

characteristic: environment (biome)

text: hydrothemal vent

characteristic: environment (feature)

text: diffuse fluid

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: hydrothermal vent metagenome

characteristic: organism

text: Axial Omics 2015

text: hydrothermal vent metagenome

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MBL

text: public

text: Diffuse fluid metagenome from the North Rift Zone, post eruption in 2015

text: marine

text: hydrothemal vent

text: diffuse fluid

text: Pacific Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hydrothermal vent metagenome

text: Axial Omics 2015

characteristic: project name

text: hydrothermal vent metagenome

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: marine

text: hydrothemal vent

text: diffuse fluid

text: Pacific Ocean

text: metagenome

text: hydrothermal vent metagenome

text: Axial Omics 2015

text: hydrothermal vent metagenome

characteristic: title

text: water


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MBL

text: public

characteristic: collection date

text: Metagenomic fluid sample from hydrothermal plume above Anemone vent, 2015

characteristic: description

text: marine

characteristic: environment (biome)

text: hydrothemal vent plume

characteristic: environment (feature)

text: hydrothermal fluid

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: hydrothermal vent metagenome

characteristic: organism

text: Axial Omics 2015

text: hydrothermal vent metagenome

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MBL

text: public

text: Metatranscriptomic fluid sample from hydrothermal plume above Anemone vent, 2015

text: marine

text: hydrothemal vent plume

text: hydrothermal fluid

text: Pacific Ocean

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: hydrothermal vent metagenome

text: Axial Omics 2015

characteristic: project name

text: hydrothermal vent metagenome

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MBL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Metagenomic sample from background seawater, off-axis, at 1500m, from 2015

text: marine

text: deep ocean

text: seawater

text: Pacific Ocean

text: metagenome

text: marine metagenome

text: Axial Omics 2015

text: marine metagenome

characteristic: title

text: water


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: MBL

text: public

characteristic: collection date

text: Metatranscriptomic sample from background seawater, off-axis, at 1500m, from 2015

characteristic: description

text: marine

characteristic: environment (biome)

text: deep ocean

characteristic: environment (feature)

text: seawater

characteristic: environment (material)

text: Pacific Ocean

characteristic: geographic location (country and/or sea)

text: metagenome

text: marine metagenome

characteristic: organism

text: Axial Omics 2015

text: marine metagenome

text: water


text: Plasmodium vivax

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: malaria parasite P. vivax

characteristic: common name

text: Plasmodium vivax

text: Plasmodium vivax


text: Universita degli studi di Milano

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Universita degli studi di Milano

text: human

text: In the sample there are all the subjects involved in this study. each reads is associated to a name of subject and the number of sample.

text: Stool samples

text: Human gut

text: stool

text: Italy

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: Effect of L. casei DG® (Lactobacillus paracasei CNCM I-1572) on symptoms, gut microbiota, short chain fatty acids, and immune activation in patients with irritable bowel syndrome: a randomized clinical trial.

characteristic: project name

text: Homo sapiens

text: Illumina MiSeq system

characteristic: sequencing method


text: Plasmodium falciparum

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum

characteristic: title


E-MTAB-5502:Mouse XdhTg

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-5502:Mouse XdhTg

tag: Namespace:IRCCS Mario Negri Institute For Pharmacological Research

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Genomic DNA from mutXDH transgenic Mouse (XdhTg). Transgenic mice were originally generated in the B6D2F1 hybrid strain (C57BL/6 X DBA2) and subsequently stabilized in C57BL/6 background by over 10 successive rounds of inter-breeding. Liver dissected from mutXDH transgenic mouse (XdhTg) DNA from liver was extracted using DNA-Mini Kit (Qiagen) and fragmented using Bioruptor (Diagenode). 380 ng DNA in 100 microL were subjected to sonication with the following parameters: power setting low, cycle 30sec on/ 90sec off, time 8 minutes in ice-cold, degassed water, resulting in average 550 bp size fragments.

characteristic: description

text: mutXDH transgenic mouse

characteristic: genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: liver

characteristic: organism part

text: glaucomatous phenotype

characteristic: phenotype

text: Mus musculus

characteristic: strain

text: Mouse XdhTg


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Linkoping University Dept. Clinical and Experimental Medicine  Center for Social and Affective Neuroscience

text: ArrayExpress

text: house mouse

characteristic: common name

text: Protocols: Brains from eighteen adult C57BL/6J(JAX) male mice (13-14 weeks old) were frozen in -80oC isopentane after cervical dislocation. 1.0 mm micro-punches were taken from the ventrolateral and dorsolateral striatum, excluding the lateral septal nucleus, but included nuclueus accumbens and most of caudate putamen; main area containing d1/2 dopamine receptors in striatum (http://www.brain-map.org/). ChIP protocols have been described elsewhere but here we applied it to individual animals; Feng J., Wilkinson M., Liu X., et al. (2014) Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biology 15, and Dias C., Feng J., Sun H et al. (2014) β-catenin mediates behavioral resilience through Dicer1/microRNA regulation. Nature 516. Frozen punches were crosslinked in with a protease inhibitor (pi) in PBS and 1% formaldehyde buffer, and after 12 min quenched with 0.125 M glycine. After washes in ice cold pi-PBS, punches were homogenized in pi-SDS lysis buffer (1%) by aspirating the punches 15 times through a syringe needle (22 gauge). An ice chilled Bioruptor standard (Diagenode) cycled 9x5 min (30 s on 30 s off; high power) was used to fragment the chromatin. Immunoprecipitation (IP) was done at 4oC overnight using the Egr-1 Antibody (C-19) X (Santa Cruz Biotechnology) bound to Dynabeads M-280 Sheep anti-Rabbit IgG (Life technologies) in diluted pi-SDS/Triton X-100 buffer. IP samples were washed in ice-cold Hepes/LiCl RIPA buffer on a magnetic rack, with a final wash in salty 1xTE buffer (with 50mM NaCl), before elution in SDS buffer. Release and decrosslinking was performed adding RNase A (1h, 37oC) and Proteinase K (2h, 55oC), followed by QiaQuick (Qiagen) clean up. IP and Input samples were treated identically but Input did not went through overnight immunoprecipitation and was pooled prior to library preparation. NEBNext Ultra™ DNA Library Prep Kit (New England Biolabs) with NEBNext Multiplex Oligos (New England Biolabs) for Illumina was used for library preparation according to manufacturer’s recommendations. Concentrations and fragment sizes were verified using High sensitivity DNA BioAnalyzer chips (Agilent). Barcoded libraries were calibrated to same concentrations, pooled, agaros gel size selected (mean fragment length of 350+/-150bp) and cleaned using QiaQuick (Qiagen).

text: Mus musculus

text: Mus musculus

text: amygdala

text: Mus musculus

text: male

characteristic: sex

text: ChIP


tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Linkoping University Dept. Clinical and Experimental Medicine Center for Social and Affective Neuroscience

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: Mus musculus

text: Mus musculus

text: amygdala

text: Mus musculus

text: male

text: Input


E-MTAB-5495:CTVT17 P

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT17 P

tag: Namespace:Department of Infection, UCL

text: ArrayExpress

characteristic: broker name

text: dog

text: Protocols: Biopsies of were collected from dogs undergoing diagnostic assessment at the Department of Surgery and Obstetrics and Gynaecology, Faculty of Veterinary Medicine, University of Messina, Italy. All the procedures on animals treated in Italy, including housing, conformed to EU regulations of animal welfare and are approved by the Italian Ministry of Health being in agreement with the directive D.P.C.M. of 28th February 2003. Qiagen AllPrep Micro kit according to the manufacturer's protocol Sonication with the Diagenode Bioruptor. Following fragmentation (180-230 bp fragments), library preparation consists of DNA end repair, 3′-dA tailing and adapter ligation. DNA was incubated with 150 ng anti-5-methylcytidine at 4°C for 15 hrs using automation and manufacturer reagents and protocols (Diagenode). Following immunoprecipitation, DNA was incubated with 1 μg proteinase K (Diagenode) at 55°C for 15 mins then 95°C for 15 mins. Each sample was subject to quality control using quantitative PCR (qPCR) with primers designed to amplify methylated/unmethylated control DNA (see https://www.ncbi.nlm.nih.gov/pubmed/22402632 for details). After confirming enrichment of methylated DNA in the immunoprecipitated fraction, DNA was purified using AmpureXT magnetic beads and amplified by 12 cycles adapter-mediated PCR. PCR products were purified using Ampure magnetic beads and run out on 2% low-melting point agarose gel. PCR fragments were excised and purified (QIAGEN). The resulting libraries (300-350 bp) were quality controlled using an Agilent 2100 Bioanalyzer with DNA1000 chips.

text: canine transmissible veneral tumour

characteristic: disease

characteristic: individual

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT17 P

characteristic: title

text: Progressive

characteristic: tumor grading


E-MTAB-5495:CTVT17 R

text: Department of Infection, UCL

characteristic: INSDC center name

text: public

text: E-MTAB-5495:CTVT17 R

text: ArrayExpress

text: dog

characteristic: description

text: canine transmissible veneral tumour

text: Canis lupus familiaris

characteristic: organism

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT17 R

text: Regressive


E-MTAB-5495:CTVT17 S

text: Department of Infection, UCL

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5495:CTVT17 S

text: ArrayExpress

text: dog

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT17 S

text: Stationary


E-MTAB-5495:CTVT5 P

characteristic: ENA-CHECKLIST

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT5 P

text: ArrayExpress

text: dog

characteristic: common name

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT5 P

text: Progressive


E-MTAB-5495:CTVT5 R

characteristic: ENA-FIRST-PUBLIC

text: Department of Infection, UCL

text: public

characteristic: SRA accession

text: E-MTAB-5495:CTVT5 R

text: ArrayExpress

text: dog

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT5 R

text: Regressive


E-MTAB-5495:CTVT5 S

characteristic: ENA-LAST-UPDATE

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT5 S

characteristic: Submitter Id

text: ArrayExpress

text: dog

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT5 S

text: Stationary


E-MTAB-5495:CTVT6 P

characteristic: External Id

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT6 P

text: ArrayExpress

characteristic: broker name

text: dog

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT6 P

text: Progressive


E-MTAB-5495:CTVT6 R

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT6 R

text: ArrayExpress

text: dog

text: canine transmissible veneral tumour

characteristic: disease

characteristic: individual

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT6 R

text: Regressive


E-MTAB-5495:CTVT6 S

text: Department of Infection, UCL

text: public

text: E-MTAB-5495:CTVT6 S

text: ArrayExpress

text: dog

text: canine transmissible veneral tumour

text: Canis lupus familiaris

text: Canis lupus familiaris

text: Canis lupus familiaris

text: CTVT6 S

characteristic: title

text: Stationary

characteristic: tumor grading


E-MTAB-5536:Meis ChIP BA2 rep1

text: UOM

characteristic: INSDC center name

text: public

text: E-MTAB-5536:Meis ChIP BA2 rep1

text: ArrayExpress

text: house mouse

text: Protocols: The preparation of the material was as described in Kutejova et al., 2008. Second branchial arches, and posterior branchial arches connected to OFT were dissected (the whole tissue), crosslinked and frozen in order to pool enough for ChIP. Kutejova E, Engist B, Self M, Oliver G, Kirilenko P, Bobola N. Six2 functions redundantly immediately downstream of Hoxa2. Development. 2008. 135(8):1463-70. PMID: 18321982. MinElute PCR purification kit (Qiagen) ChIP-seq was performed as described in Donaldson et al., 2012, using 20ug of Meis antibody (Santa Cruz Biotechnology sc-10599X). Donaldson I, Amin S, Hensman J, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward C and Bobola N. Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development. Nucleic Acids Res. 2012. 40(9):3990-4001. 70 arches were used for each sample. Library preparation was performed using the TruSeq ChIP Sample Preparation kit (Illumina).

characteristic: description

text: embryonic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: second branchial arch

characteristic: organism part

text: Mus musculus

characteristic: strain

text: Meis ChIP BA2 rep1


E-MTAB-5536:Meis ChIP BA2 rep2

characteristic: ENA-CHECKLIST

text: UOM

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-5536:Meis ChIP BA2 rep2

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: second branchial arch

text: Mus musculus

text: Meis ChIP BA2 rep2


E-MTAB-5536:Meis ChIP PBA rep1

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UOM

text: public

characteristic: SRA accession

text: E-MTAB-5536:Meis ChIP PBA rep1

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 11.5

text: Mus musculus

text: Mus musculus

text: posterior branchial arches connected to OFT

text: Mus musculus

text: Meis ChIP PBA rep1


E-MTAB-5536:Meis ChIP PBA rep2

characteristic: External Id

text: UOM

text: public

text: E-MTAB-5536:Meis ChIP PBA rep2

text: ArrayExpress

characteristic: broker name

text: house mouse

text: embryonic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meis ChIP PBA rep2

characteristic: title


E-MTAB-5536:Meis Input BA2 rep1

text: UOM

characteristic: INSDC center name

text: public

text: E-MTAB-5536:Meis Input BA2 rep1

text: ArrayExpress

text: house mouse

characteristic: description

text: embryonic day 11.5

text: Mus musculus

text: Mus musculus

text: second branchial arch

text: Mus musculus

text: Meis Input BA2 rep1


E-MTAB-5536:Meis Input BA2 rep2

text: UOM

text: public

text: E-MTAB-5536:Meis Input BA2 rep2

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: second branchial arch

characteristic: organism part

text: Mus musculus

text: Meis Input BA2 rep2


E-MTAB-5536:Meis Input PBA rep1

characteristic: ENA-CHECKLIST

text: UOM

text: public

text: E-MTAB-5536:Meis Input PBA rep1

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

characteristic: strain

text: Meis Input PBA rep1


E-MTAB-5536:Meis Input PBA rep2

text: UOM

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5536:Meis Input PBA rep2

text: ArrayExpress

text: house mouse

text: embryonic day 11.5

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Meis Input PBA rep2


L. plantarum A6

text: UNIVERSITY OF TORONTO

text: public

characteristic: INSDC status

text: L. plantarum A6

tag: Namespace:UNIVERSITY OF TORONTO

text: Lactobacillus plantarum

characteristic: organism

text: Lactobacillus plantarum

text: The genomic and transcriptomic basis of the nutritional potential of Lactobacillus plantarum A6 in a food matrix


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERSITY

text: public

tag: Namespace:OREGON STATE UNIVERSITY

text: American beaver

text: Castor canadensis

text: Castor canadensis

text: blood

characteristic: tissue type

text: Beaver Genome Project


text: SIB

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Full genome assembly of strain JF4335 of Clostridium chauvoeii.

text: Switzerland

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Bos taurus

characteristic: host scientific name

characteristic: isolate

text: Isolated from cattle with blackleg

characteristic: isolation source

text: Clostridium chauvoei JF4335

text: Clostridium chauvoei JF4335


CECT 5396

characteristic: ENA-CHECKLIST

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 5396

text: host associated

characteristic: environment (biome)

text: stationary culture of dinoflagellate

characteristic: environment (feature)

text: dinoflagellate Prorocentrum lima

characteristic: environment (material)

text: Spain

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Marinovum algicola

text: Whole genome sequencing of Marinovum algicola CECT 5396, type strain

characteristic: project name

text: Marinovum algicola

text: Illumina Miseq

characteristic: sequencing method

text: CECT 5396

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: epithelial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: MCF-7/SP10+ and MCF-7/C breast cancer cells were routinely cultured in a humidified 95% air/5% CO2 incubator at 37 °C in complete medium Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS) 1.0 mM sodium pyruvate, 2mM L-glutamine and 100 IU/mL penicillin. The low metastatic MCF-7 (ERα positive) epithelial breast cancer cells were transfected with transduction ready lentiviral particles containing short hairpin RNA (shRNA) against ERα (MCF-7/SP10+) and with control shRNA lentiviral particles that encode a scrambled shRNA sequence (MCF-7/C) Total RNA was isolated from cells using NucleoSpin® RNA plus Kit (Macherey-Nagel). The amount of isolated RNA was quantified by measuring its absorbance at 260 nm. Total RNA for AmpliSeq analysis was extracted in 3 biological replicates and 3 technical replicates as described above. 50 ng of RNA were reverse transcribed to cDNA using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit Preparation protocol (Revision A.0, Thermo Fisher). The acquired cDNA was amplified using Ion AmpliSeq™ Transcriptome Human Gene Expression core panel (Thermo Fisher) and the primer sequences were then partially digested. Then, DNA adaptors (Ion P1 Adaptor and Ion Xpress™ Barcode Adaptor, Thermo Fisher) were ligated to the amplicons. Adaptor ligated amplicons were purified using the Agencourt® AMPure® XP reagent (Beckman Coulter) and eluted in amplification mix (Platinum® PCR SuperMix High Fidelity and Library Amplification Primer Mix, Thermo Fisher) and amplified. Size-selection and purification was conducted using Agencourt® AMPure® XP reagent (Beckman Coulter). The amplicons were quantified using the Fragment AnalyzerTM instrument (Advanced Analytical Technologies, INC.) with DNF-474 High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies, INC.). Samples were then pooled, six or less per pool, followed by emulsion PCR on either the Ion OneTouch™ 2 System using the Ion PI™ Hi-Q™ OT2 Kit (Thermo Fisher), or on the Ion Chef™ System using the Ion PI Hi-Q Chef Kit (Thermo Fisher). The pooled samples were loaded on Ion PI™ v3 chips and sequenced on the Ion Proton™ System using the Ion PI™ Hi-Q Sequencing 200 Kit chemistry (200 bp read length, Thermo Fisher). Mean read length was 114 bp.

characteristic: description

text: breast adenocarcinoma

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: estrogen receptor alpha positive

characteristic: phenotype

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University

characteristic: INSDC center name

text: public

text: ArrayExpress

text: epithelial cell

text: human

text: breast adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: estrogen receptor alpha positive

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: epithelial cell

text: human

text: breast adenocarcinoma

text: Homo sapiens

text: Homo sapiens

text: estrogen receptor alpha negative

text: Homo sapiens

characteristic: title


CECT 7023

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CECT 7023

characteristic: collection date

text: water

characteristic: environment (biome)

text: water

characteristic: environment (feature)

text: water

characteristic: environment (material)

text: Antarctica

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Roseisalinus antarcticus

text: Whole genome sequencing of Roseisalinus antarcticus CECT 7023, type strain

characteristic: project name

text: Roseisalinus antarcticus

text: Illumina Miseq

characteristic: sequencing method

text: CECT 7023

characteristic: strain

text: water

characteristic: water environmental package


CECT 7066

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: CECT 7066

characteristic: Submitter Id

text: Sediment

text: Sediment

text: Saline soil bordering a saltern

text: Spain

characteristic: geographic location (elevation)

text: mimarks-survey

text: Palleronia marisminoris

characteristic: organism

text: Whole genome sequencing of Palleronia marisminoris CECT 7066, type strain

text: Palleronia marisminoris

text: sediment

characteristic: sediment environmental package

text: Illumina Miseq

text: CECT 7066

characteristic: title


CECT 7450

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CECT 7450

characteristic: collection date

text: Seawater

characteristic: environment (biome)

text: Seawater

characteristic: environment (feature)

text: Seawater obtained off coast of Vinaroz

characteristic: environment (material)

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: Roseovarius albus

text: Whole genome sequencing of Roseovarius albus CECT 7450, type strain

text: Roseovarius albus

text: Illumina Miseq

text: CECT 7450

text: water


CECT 7680

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

characteristic: SRA accession

text: CECT 7680

text: Seawater

text: Seawater

text: Seawater from Hwajinpo

text: South Korea

text: mimarks-survey

characteristic: investigation type

text: Pseudoruegeria aquimaris

text: Whole genome sequencing of Pseudoruegeria aquimaris CECT 7680, type strain

characteristic: project name

text: Pseudoruegeria aquimaris

text: Illumina Miseq

characteristic: sequencing method

text: CECT 7680

characteristic: strain

text: water

characteristic: water environmental package


CECT 7691

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: CECT 7691

characteristic: Submitter Id

characteristic: collection date

text: Host associated

characteristic: environment (biome)

text: Wild long-snouted seahorses

characteristic: environment (feature)

text: Cutaneous mucus of wild long-snouted seahorses (Hippocampus guttulatus) captured in northwest Spain

text: Spain

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

text: Oceanibacterium hippocampi

characteristic: organism

text: Whole genome sequencing of Oceanibacterium hippocampi CECT 7691, type strain

text: Oceanibacterium hippocampi

text: Illumina Miseq

text: CECT 7691

characteristic: title


CECT 7745

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 7745

text: Seawater

text: Seawater

text: Yellow Sea tidal flat

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: Roseovarius aestuarii

text: Whole genome sequencing of Roseovarius aestuarii CECT 7745, type strain

text: Roseovarius aestuarii

text: Illumina Miseq

text: CECT 7745

text: water


text: Institute of Clinical Molecular Biology

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Institute of Clinical Molecular Biology

characteristic: Submitter Id

text: Ancient metagenome sample

characteristic: description

text: fossil metagenome

text: fossil metagenome

text: Generic sample from Ancient metagenome sample


CECT 7751

text: UVEG

text: public

text: CECT 7751

characteristic: collection date

text: Seawater

characteristic: environment (biome)

text: Seawater

characteristic: environment (feature)

text: Seawater from Eluanbi coast

text: Taiwan

text: mimarks-survey

characteristic: investigation type

text: Pseudooceanicola marinus

characteristic: organism

text: Whole genome sequencing of Pseudooceanicola marinus CECT 7751, type strain

characteristic: project name

text: Pseudooceanicola marinus

text: Illumina Miseq

characteristic: sequencing method

text: CECT 7751

characteristic: strain

characteristic: title

text: water

characteristic: water environmental package


CECT 7971

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 7971

text: Seawater

text: Seawater

text: Seawater of the Yellow Sea

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

text: Pacificibacter marinus

text: Whole genome sequencing of Pacificibacter marinus CECT 7971, type strain

text: Pacificibacter marinus

text: Illumina Miseq

text: CECT 7971

text: water


text: Institute of Tropical Medicine

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Institute of Tropical Medicine

characteristic: Submitter Id

characteristic: collection date

text: Democratic Republic of the Congo

text: diseased

characteristic: host health state

text: Homo Sapiens

characteristic: host scientific name

characteristic: isolate

text: human blood

characteristic: isolation source

text: Salmonella enterica subsp. enterica serovar Typhi

text: Typhi

characteristic: serovar