text: public

tag: Namespace:Centre de Biologie pour la Gestion des Populations (CBGP - UMR1062)

text: Armelle Coeur D'acier

characteristic: collected by

characteristic: collection date

text: Pinus strobus

characteristic: host scientific name

text: Armelle Coeur D'acier

characteristic: identified by

characteristic: isolate

text: tree branch; tree trunk

characteristic: isolation source

text: 47.2017 N 94.9925 W

characteristic: lat lon

text: Cinara strobi

text: Cinara strobi

characteristic: specimen voucher

text: Genome sequencing of the endosymbiotic consortium and mitochondrion of Cinara strobi species voucher 3249


status: PUBLIC

text: Bacillus simplex

tag: attribute

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Bacillus simplex

characteristic: common name

text: Bacillus simplex

characteristic: organism

text: Bacillus simplex

characteristic: strain

characteristic: title


text: SC

text: public

characteristic: anonymized name

characteristic: collection date

text: Bacteroides thetaiotaomicron

characteristic: culture collection

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

characteristic: isolation source

text: Bacteroides thetaiotaomicron

text: Bacteroides thetaiotaomicron

text: not available: to be reported later

characteristic: serovar

text: not available: to be reported later

characteristic: specific host


text: Bordetella pseudohinzii

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Bordetella pseudohinzii

text: Bordetella pseudohinzii

text: Bordetella pseudohinzii


text: Capnocytophaga leadbetteri

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Capnocytophaga leadbetteri

characteristic: common name

text: Capnocytophaga leadbetteri

characteristic: organism

text: Capnocytophaga leadbetteri


text: Cronobacter sakazakii

text: SC

text: public

text: Cronobacter sakazakii

text: Cronobacter sakazakii

text: Cronobacter sakazakii

characteristic: strain

characteristic: title


text: Enterococcus durans

text: SC

text: public

text: Enterococcus durans

text: Enterococcus durans

text: Enterococcus durans


text: Francisella tularensis subsp. holarctica

text: SC

text: public


text: Listeria grayi

text: SC

text: public

text: Listeria grayi

text: Listeria grayi

text: Listeria grayi


text: Mycoplasma canis

text: SC

text: public

text: Mycoplasma canis

text: Mycoplasma canis

text: Mycoplasma canis


text: Salmonella bongori

text: SC

text: public

text: Salmonella bongori

text: Salmonella bongori

text: Salmonella bongori


text: Salmonella enterica subsp. enterica serovar Paratyphi A

text: SC

text: public


text: Salmonella enterica subsp. enterica serovar Paratyphi C

text: SC

text: public


text: Salmonella enterica subsp. enterica serovar Typhi

text: SC

text: public


text: Vibrio cholerae non-O1

text: SC

text: public

text: Vibrio cholerae non-O1

text: Vibrio cholerae non-O1

text: Vibrio cholerae non-O1


text: Weissella viridescens

text: SC

text: public

text: Weissella viridescens

text: Weissella viridescens

text: Weissella viridescens


text: Enterococcus faecalis

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


text: Staphylococcus massiliensis

text: SC

text: public

text: Staphylococcus massiliensis

text: Staphylococcus massiliensis

text: Staphylococcus massiliensis


text: Prevotella melaninogenica

text: SC

text: public

text: Prevotella melaninogenica

text: Prevotella melaninogenica

text: Prevotella melaninogenica


text: Burkholderia stabilis

text: SC

text: public

text: Burkholderia stabilis

text: Burkholderia stabilis

text: Burkholderia stabilis


text: Clostridium perfringens

text: SC

text: public

text: Clostridium perfringens

text: Clostridium perfringens

text: Clostridium perfringens


text: Pandoraea apista

text: SC

text: public

text: Pandoraea apista

text: Pandoraea apista

text: Pandoraea apista


text: Pandoraea norimbergensis

text: SC

text: public

text: Pandoraea norimbergensis

text: Pandoraea norimbergensis

text: Pandoraea norimbergensis


text: Actinobacillus pleuropneumoniae

text: SC

text: public

text: Actinobacillus pleuropneumoniae

text: Actinobacillus pleuropneumoniae

text: Actinobacillus pleuropneumoniae


text: Paeniclostridium sordellii

text: SC

text: public

text: Paeniclostridium sordellii

text: Paeniclostridium sordellii

text: Paeniclostridium sordellii


text: Neisseria flavescens

text: SC

text: public

text: Neisseria flavescens

text: Neisseria flavescens

text: Neisseria flavescens


text: Bordetella bronchiseptica

text: SC

text: public

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica


text: Escherichia coli

text: SC

text: public

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli


text: Kocuria varians

text: SC

text: public

text: Kocuria varians

text: Kocuria varians

text: Kocuria varians


text: Enterococcus raffinosus

text: SC

text: public

text: Enterococcus raffinosus

text: Enterococcus raffinosus

text: Enterococcus raffinosus


text: Enterococcus faecium

text: SC

text: public

text: Enterococcus faecium

text: Enterococcus faecium

text: Enterococcus faecium


text: Streptococcus constellatus

text: SC

text: public

text: Streptococcus constellatus

text: Streptococcus constellatus

text: Streptococcus constellatus


text: Streptococcus agalactiae

text: SC

text: public

text: Streptococcus agalactiae

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Streptococcus lutetiensis

text: SC

text: public

text: Streptococcus lutetiensis

text: Streptococcus lutetiensis

text: Streptococcus lutetiensis


text: Enterococcus faecalis

text: SC

text: public

text: Enterococcus faecalis

text: Enterococcus faecalis

text: Enterococcus faecalis


text: Enterococcus avium

text: SC

text: public

text: Enterococcus avium

text: Enterococcus avium

text: Enterococcus avium


text: Streptococcus dysgalactiae subsp. equisimilis

text: SC

text: public


text: Streptococcus dysgalactiae

text: SC

text: public

text: Streptococcus dysgalactiae

text: Streptococcus dysgalactiae

text: Streptococcus dysgalactiae


text: Streptococcus mutans

text: SC

text: public

text: Streptococcus mutans

text: Streptococcus mutans

text: Streptococcus mutans


text: Streptococcus suis

text: SC

text: public

text: Streptococcus suis

text: Streptococcus suis

text: Streptococcus suis


text: Romboutsia ilealis

text: SC

text: public

text: Romboutsia ilealis

text: Romboutsia ilealis

text: Romboutsia ilealis


text: Lactobacillus plantarum

text: SC

text: public

text: Lactobacillus plantarum

text: Lactobacillus plantarum

text: Lactobacillus plantarum


text: Mycobacterium barrassiae

text: SC

text: public

text: Mycobacterium barrassiae

text: Mycobacterium barrassiae

text: Mycobacterium barrassiae


text: Campylobacter upsaliensis

text: SC

text: public

text: Campylobacter upsaliensis

text: Campylobacter upsaliensis

text: Campylobacter upsaliensis


text: Cardiobacterium sp. A

text: SC

text: public

text: Cardiobacterium sp. A

text: Cardiobacterium sp. A

text: Cardiobacterium sp. A


text: Porphyromonas circumdentaria

text: SC

text: public

text: Porphyromonas circumdentaria

text: Porphyromonas circumdentaria

text: Porphyromonas circumdentaria


text: Helicobacter pylori

text: SC

text: public

text: Helicobacter pylori

text: Helicobacter pylori

text: Helicobacter pylori


text: Pseudomonas fluorescens

text: SC

text: public

text: Pseudomonas fluorescens

text: Pseudomonas fluorescens

text: Pseudomonas fluorescens


text: Pseudomonas mendocina

text: SC

text: public

text: Pseudomonas mendocina

text: Pseudomonas mendocina

text: Pseudomonas mendocina


text: Pseudomonas guguanensis

text: SC

text: public

text: Pseudomonas guguanensis

text: Pseudomonas guguanensis

text: Pseudomonas guguanensis


text: Weeksella virosa

text: SC

text: public

text: Weeksella virosa

text: Weeksella virosa

text: Weeksella virosa


text: Capnocytophaga sp. oral taxon 326

text: SC

text: public

text: Capnocytophaga sp. oral taxon 326

text: Capnocytophaga sp. oral taxon 326

text: Capnocytophaga sp. oral taxon 326


text: Capnocytophaga sp. oral taxon 412

text: SC

text: public

text: Capnocytophaga sp. oral taxon 412

text: Capnocytophaga sp. oral taxon 412

text: Capnocytophaga sp. oral taxon 412


text: Campylobacter lari subsp. lari

text: SC

text: public

text: Campylobacter lari subsp. lari

text: Campylobacter lari subsp. lari

text: Campylobacter lari subsp. lari


text: Legionella dresdenensis

text: SC

text: public

text: Legionella dresdenensis

text: Legionella dresdenensis

text: Legionella dresdenensis


text: Moraxella caprae

text: SC

text: public

text: Moraxella caprae

text: Moraxella caprae

text: Moraxella caprae


text: Shigella sonnei

text: SC

text: public

text: Shigella sonnei

text: Shigella sonnei

text: Shigella sonnei


text: Klebsiella pneumoniae

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae


text: Haemophilus haemolyticus

text: SC

text: public

text: Haemophilus haemolyticus

text: Haemophilus haemolyticus

text: Haemophilus haemolyticus


text: Salmonella enterica subsp. enterica

text: SC

text: public

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica

text: Salmonella enterica subsp. enterica


text: Salmonella enterica

text: SC

text: public

text: Salmonella enterica

text: Salmonella enterica

text: Salmonella enterica


text: Chryseobacterium shandongense

text: SC

text: public

text: Chryseobacterium shandongense

text: Chryseobacterium shandongense

text: Chryseobacterium shandongense


text: Comamonas kerstersii

text: SC

text: public

text: Comamonas kerstersii

text: Comamonas kerstersii

text: Comamonas kerstersii


text: Fusobacterium nucleatum

text: SC

text: public

text: Fusobacterium nucleatum

text: Fusobacterium nucleatum

text: Fusobacterium nucleatum


text: Haemophilus influenzae

text: SC

text: public

text: Haemophilus influenzae

text: Haemophilus influenzae

text: Haemophilus influenzae


text: Bisgaard taxon 40

text: SC

text: public

text: Bisgaard taxon 40

text: Bisgaard Taxon 40

text: Bisgaard Taxon 40


text: Chelonobacter oris

text: SC

text: public

text: Chelonobacter oris

text: Chelonobacter oris

text: Chelonobacter oris


text: Avibacterium gallinarum

text: SC

text: public

text: Avibacterium gallinarum

text: Avibacterium gallinarum

text: Avibacterium gallinarum


text: Porphyromonas circumdentaria

text: SC

text: public

text: Porphyromonas circumdentaria

text: Porphyromonas circumdentaria

text: Porphyromonas circumdentaria


text: Universite de Grenoble Alpes

text: public

tag: Namespace:Universite de Grenoble Alpes

text: Escherichia coli REL606

characteristic: isolate

text: Escherichia coli REL606

characteristic: receipt date

text: Escherichia coli REL606

text: Escherichia coli REL606


text: Pseudomonas aeruginosa

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: OX

text: public

characteristic: broker name

characteristic: description

text: Streptococcus agalactiae

text: Streptococcus agalactiae


text: Aeromonas hydrophila

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Aeromonas hydrophila

text: Aeromonas hydrophila

text: Aeromonas hydrophila


text: Moraxella nonliquefaciens

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Moraxella nonliquefaciens

text: Moraxella nonliquefaciens

text: Moraxella nonliquefaciens


text: Propionibacterium acnes

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Propionibacterium acnes

characteristic: common name

text: Cutibacterium acnes

characteristic: organism

text: Cutibacterium acnes

characteristic: subject id

characteristic: title


text: Veillonella caviae

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Veillonella caviae

text: Veillonella caviae

text: Veillonella caviae


text: Porphyromonas gingivalis

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: Porphyromonas gingivalis

text: Porphyromonas gingivalis

text: Porphyromonas gingivalis


text: Campylobacter fetus subsp. venerealis

text: SC

text: public

text: Campylobacter fetus subsp. venerealis

text: Campylobacter fetus subsp. venerealis

text: Campylobacter fetus subsp. venerealis


text: Legionella fairfieldensis

text: SC

text: public

text: Legionella fairfieldensis

text: Legionella fairfieldensis

text: Legionella fairfieldensis


text: Brevibacillus laterosporus

text: SC

text: public

text: Brevibacillus laterosporus

text: Brevibacillus laterosporus

text: Brevibacillus laterosporus


text: Pasteurella pneumotropica

text: SC

text: public

text: Pasteurella pneumotropica

text: Rodentibacter pneumotropicus

text: Rodentibacter pneumotropicus


text: Propionibacterium lymphophilum

text: SC

text: public

text: Propionibacterium lymphophilum

text: Propionimicrobium lymphophilum

text: Propionimicrobium lymphophilum


text: Actinobacillus ureae

text: SC

text: public

text: Actinobacillus ureae

text: Actinobacillus ureae

text: Actinobacillus ureae


text: Legionella santicrucis

text: SC

text: public

text: Legionella santicrucis

text: Legionella santicrucis

text: Legionella santicrucis


text: Campylobacter sputorum biovar sputorum

text: SC

text: public

text: Campylobacter sputorum biovar sputorum

text: Campylobacter sputorum biovar sputorum

text: Campylobacter sputorum biovar sputorum


text: Pasteurella skyensis

text: SC

text: public

text: Pasteurella skyensis

text: Pasteurella skyensis

text: Pasteurella skyensis


text: UNIVERSITY HOHENHEIM

text: public

tag: Namespace:UNIVERSITY HOHENHEIM

text: ceca digesta;Protease A, low level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Protease C, high level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Protease B, high level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Basal diet

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Protease A, high level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Phytase

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Protease B, low level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: UNIVERSITY HOHENHEIM

text: public

text: ceca digesta;Protease C, low level

text: chicken gut metagenome

text: chicken gut metagenome

text: Sample


text: TU Graz

text: public

tag: Namespace:TU Graz

characteristic: collection date

text: Brassicaceae

characteristic: environment (biome)

text: area of developed space with low usage intensity

characteristic: environment (feature)

text: agricultural environmental material

characteristic: environment (material)

text: Austria

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

characteristic: investigation type

text: Eruca vesicaria subsp. sativa

text: plant-associated

characteristic: plant-associated environmental package

text: Arugula microbiome

characteristic: project name

text: Eruca vesicaria subsp. sativa

text: 454 pyrosequencing

characteristic: sequencing method

text: Arugula microbiome


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Centre de Biologie pour la Gestion des Populations (CBGP - UMR1062)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Armelle Coeur d'acier

characteristic: collected by

text: Serratia symbiotica strain SeCistrobi isolate 3249 endosymbiont of the aphid Cinara strobi

characteristic: description

text: Cinara strobi

characteristic: host scientific name

characteristic: isolate

text: host's whole body

characteristic: isolation source

text: 47.2017 N 94.9925 W

characteristic: lat lon

text: Serratia symbiotica

text: Serratia symbiotica

characteristic: specimen voucher

text: SeCistrobi

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

text: Armelle Coeur D'acier

characteristic: collection date

text: Buchnera aphidicola strain BuCistrobi isolate 3249 endosymbiont of the aphid Cinara strobi

text: Cinara strobi

text: host's whole body

text: 47.2017 N 94.9925 W

text: Buchnera aphidicola (Cinara strobi)

characteristic: organism

text: Buchnera aphidicola (Cinara strobi)

text: BuCistrobi

characteristic: title


text: Mycobacterium nonchromogenicum

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Mycobacterium nonchromogenicum

characteristic: common name

text: Mycobacterium nonchromogenicum

text: Mycobacterium nonchromogenicum


text: Streptococcus porcinus

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus porcinus

text: Streptococcus porcinus

text: Streptococcus porcinus


text: Mycoplasma molare

text: SC

text: public

text: Mycoplasma molare

text: Mycoplasma molare

text: Mycoplasma molare

characteristic: strain


text: Aerococcus viridans

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Aerococcus viridans

text: Aerococcus viridans

text: Aerococcus viridans


E-MTAB-6679:Sample 1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-6679:Sample 1

tag: Namespace:Institute for Regenerative Medicine and Biotherapy

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: induced pluripotent stem cell

characteristic: cell type

text: human

text: Protocols: The undifferentiated hiPS cell line (ChiPSC-4) was derived from fibroblasts of healthy human donors and reprogrammed by using polycistronic retrovirus, based on the transduction of Oct3/4, Sox2, Klf4, and c-Myc transcription factors. The day 6 and day 13 hiPSCs-OSPCs were produced by stepwise differentiation of hiPSCs in adherent monolayer cultures. Total RNA were extracted from cells using the PureLink® RNA Mini Kit (Life Technologies) according to manufacturer’s instructions. The RNAseq libraries are constructed according to the TrueSeq Stranded (Illumina) protocol, using 500ng of total RNA

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: fibroblast

characteristic: progenitor cell type

text: Homo sapiens

text: Sample 1


E-MTAB-6679:Sample 2

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute for Regenerative Medicine and Biotherapy

text: public

text: E-MTAB-6679:Sample 2

text: ArrayExpress

text: cochlear hair cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens

text: Sample 2

characteristic: title


E-MTAB-6679:Sample 3

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6679:Sample 3

text: ArrayExpress

text: cochlear hair cell

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: induced pluripotent stem cell

text: Homo sapiens

text: Sample 3


E-MTAB-6680:D8 1

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6680:D8 1

tag: Namespace:Division of Computational Biology, University of Dundee

characteristic: Submitter Id

text: ArrayExpress

text: neural progenitor cell

text: human

text: Protocols: Human ES cells (H9, sa181, sa121) and human iPS cells (ChIPS4) were maintained as feeder-free cultures in DEF-based medium (Cellartis DEF-CS) supplemented with bFGF (30 ng/mL, Peprotech) and Noggin (10 ng/ml,Peprotech) on fibronectin coated plates, and enzymatically passaged using 13TryLE select (thermofisher). For passaging, the medium was supplemented by addition of the Rho kinase inhibitor Y-27632 (10 mM, Tocris). For differentiation assays, PSC were plated on Geltrex matrix (20μg/cm2,LifeTechnologies) at a density of 40000 cells/cm2 and shifted to N2B27medium after 24h. Cells are differentiated for 3 days in N2B27 supplemented by 3 μM Chiron99021 (Tocris) and 20 ng/ml bFgf (PeproTech) to obtain NMPs.For further differentiation, NMPs were passaged using PBS-EDTA 0.5 mM and seeded back at controlled density (200000 cells cm2) on Geltrex (20μgcm2,LifeTechnologies) in the presence of Y-27632 (10 mM, Tocris). From passaging, cells are then cultured in N2B27 containing 100 nM RA for the indicated time to obtain later stage progenitors. In addition to the above, 50 ng/mL Nogginand 10μM SB431542 are added from day 2 to day 4. Total RNA was extracted using the RNEasy mini kit (Qiagen), following themanufacturer’s instructions, with the addition of a DNAse digestion stepperformed on the column for 15 min with RQ1-DNase (Promega). RNAconcentration was measured on a Qubit device using Qubit RNA BR assay kit(ThermoFisher), and quality was checked on a TapeStation instrument(Agilent). Individually labelled libraries were prepared from 1 μg of RNA per sample using the TruSeq® Stranded mRNA Library prep kit (Illumina), according to the manufacturer’s instruction. 2 μL of Spike-ins (1/100 dilution ERCC Spike-in controls Mix1) was added per sample.

text: normal

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: replicate

text: Homo sapiens

text: D8 1


E-MTAB-6680:D8 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Division of Computational Biology, University of Dundee

text: public

text: E-MTAB-6680:D8 4

text: ArrayExpress

characteristic: broker name

characteristic: cell line

text: neural progenitor cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

text: D8 4


E-MTAB-6680:sd3/nmp 1

text: public

text: E-MTAB-6680:sd3/nmp 1

text: ArrayExpress

text: neuromesodermal progenitor cell

characteristic: cell type

text: human

characteristic: description

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: progenitor cell type

text: Homo sapiens

text: sd3/nmp 1


E-MTAB-6680:sd3/nmp 3

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: E-MTAB-6680:sd3/nmp 3

text: ArrayExpress

text: neuromesodermal progenitor cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

text: sd3/nmp 3

characteristic: title


E-MTAB-6680:sd3/nmp 4

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-6680:sd3/nmp 4

text: ArrayExpress

text: neuromesodermal progenitor cell

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

text: Homo sapiens

text: sd3/nmp 4


E-MTAB-6680:sd3/npm 2

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-6680:sd3/npm 2

characteristic: Submitter Id

text: ArrayExpress

text: neuromesodermal progenitor cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: embryonic stem cell

characteristic: replicate

text: Homo sapiens

text: sd3/npm 2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UCL

text: public

text: UCL

characteristic: collecting institution

characteristic: collection date

text: Charlotte Houldcroft

characteristic: collector name

text: Adenovirus A31 sequenced from blood

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Human adenovirus 31

text: Human adenovirus 31

text: Adenovirus from clinical specimens

characteristic: virus identifier


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: UCL

text: Charlotte Houldcroft

text: Adenovirus A31 sequenced from urine

characteristic: description

text: United Kingdom

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: Human adenovirus 31

characteristic: organism

text: Human adenovirus 31

text: Adenovirus from clinical specimens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UCL

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: UCL

characteristic: collecting institution

characteristic: collection date

text: Charlotte Houldcroft

characteristic: collector name

text: Adenovirus A31 sequenced from a throat swab

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: Human adenovirus 31

text: Human adenovirus 31

text: Adenovirus from clinical specimens


characteristic: ENA-LAST-UPDATE

text: GSK (GlaxoSmithKline)

text: public

tag: Namespace:GSK (GlaxoSmithKline)

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: All donors provided written informed consent for use of their material, and the collection and use of the samples received Institutional Review Board review and approval. Of the seventeen synovial biopsy samples progressed for RNA-Seq and DNA methylation analyses, fifteen were obtained from knee and two from ankle. Samples were collected from 6 male and 11 female patients and under different medication regimens: no medication, non-steroid anti-inflammatory drugs (NSAID), conventional and biological disease-modifying anti-rheumatic drugs (CDMARD and BDMARD), and combinations thereof. All patients underwent arthroscopic synovial tissue biopsy sampling of an actively inflamed knee joint or ankle. Samples were flash frozen upon collection. Synovial biopsies were disrupted and homogenised in Buffer RLT Plus and β-mercaptoethanol (β-ME) using QIAshredder spin columns followed by simultaneous isolation of DNA and Total RNA using a AllPrep DNA/RNA Mini kit (Qiagen). RNA samples were quantified and their integrity assessed using Qubit RNA Broad Range Assay Kit (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies) respectively. Depending on sample yield, DNA samples were quantified using Qubit DNA BR or Qubit DNA HS kit (Thermo Fisher Scientific). RNA-Seq libraries were prepared using TruSeq® Stranded Total RNA LT - (with Ribo-Zero™ Human/Mouse/Rat) - Set A kit (Illumina), per manufacturer’s protocol except for two modifications. First, the time of ‘Elution 2 - Frag - Prime’ program was reduced from 8 to 6 min to increase the length of the RNA fragments. Secondly, the number of cycles (11 instead of 15) and the time of the initial step in each cycle (30 instead of 10 sec at the first 98°C step) were both modified to minimize PCR-based amplification bias (‘PCR’ program). Two rounds of qPCR quantification of the final libraries were performed with the KAPA Library Quantification Kit (KAPA Biosystems) on a QuantStudio 12K Flex Real-Time PCR System (Thermo Fisher Scientific).

text: rheumatoid arthritis

characteristic: disease

characteristic: individual

characteristic: institute

text: CDMARD

characteristic: medication

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

characteristic: organism part

text: knee

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

characteristic: swollen joint count


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: GSK (GlaxoSmithKline)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: rheumatoid arthritis

text: CDMARD and BDMARD

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

text: GSK (GlaxoSmithKline)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: rheumatoid arthritis

characteristic: disease

characteristic: individual

characteristic: institute

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: female

text: high

characteristic: swelling


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: GSK (GlaxoSmithKline)

text: public

text: ArrayExpress

text: human

text: rheumatoid arthritis

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

characteristic: organism part

text: knee

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex

text: low

characteristic: swollen joint count


text: GSK (GlaxoSmithKline)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: rheumatoid arthritis

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: male

text: high


characteristic: ENA-LAST-UPDATE

text: GSK (GlaxoSmithKline)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: rheumatoid arthritis

characteristic: disease

characteristic: individual

text: NSAID

characteristic: medication

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: female

text: low

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: GSK (GlaxoSmithKline)

text: public

text: ArrayExpress

text: human

text: rheumatoid arthritis

characteristic: institute

text: NSAID

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

characteristic: organism part

text: knee

characteristic: sampling site

text: Homo sapiens

text: female

characteristic: sex


text: GSK (GlaxoSmithKline)

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: rheumatoid arthritis

text: NSAID

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

text: ankle

text: Homo sapiens

text: male

text: high

characteristic: swelling

characteristic: swollen joint count


characteristic: ENA-LAST-UPDATE

text: GSK (GlaxoSmithKline)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: rheumatoid arthritis

characteristic: disease

characteristic: individual

text: NSAID and CDMARD

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text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: female

text: low


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: GSK (GlaxoSmithKline)

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text: ArrayExpress

text: human

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characteristic: institute

text: NSAID and CDMARD

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

characteristic: organism part

text: ankle

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text: Homo sapiens

text: male

characteristic: sex

characteristic: title


text: GSK (GlaxoSmithKline)

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: human

characteristic: description

text: rheumatoid arthritis

text: NSAID, CDMARD and BDMARD

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: female

characteristic: swollen joint count


characteristic: ENA-LAST-UPDATE

text: GSK (GlaxoSmithKline)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: rheumatoid arthritis

characteristic: disease

characteristic: individual

text: NSAID, CDMARD and BDMARD

characteristic: medication

text: Homo sapiens

text: Homo sapiens

text: synovial membrane

text: knee

text: Homo sapiens

text: male

text: high

characteristic: swelling


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_6D8BAFD2-9D52-49B1-9ECE-7062F4DA2716

tag: Namespace:European Centre for Disease Prevention and Control

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

text: European Centre for Disease Prevention and Control

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_B5A26222-957C-4499-BF16-5FD0A5F84358

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_17A484BF-C0C0-4F8D-853D-094BB4F07287

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_98782401-7D29-48AE-BBD3-458551F12601

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_325088AA-1CE7-4F93-9C39-92E5EB5405FE

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

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text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_B331C964-231A-4661-8912-DDAA0E788D2C

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_65985109-50C8-48CC-80CE-6639A9B112D9

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_7D0DF8A4-843D-44A3-AFD0-4C44653663DB

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_4139C34E-CBE9-4EA6-834D-83864F9899D6

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_C34A06BF-BA35-4615-BBCF-F14BB5E1E88E

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_852D647C-1113-4BE7-B23C-7D4AE5C28AD1

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_E4712040-ECE4-43EF-B3D0-EA7DC4382AB4

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_D6BA03F3-08E8-4BF1-BA62-4F7A0B421A51

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_0C042FC5-F318-42EA-BC54-AD85E6DC174D

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_FC6B4DB6-D8C5-4F07-8840-C713A28F36B5

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_E99E75B1-E14B-4548-85FF-2F6885535080

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_1567A602-77B5-492B-A973-2393D10ED9A0

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: European Centre for Disease Prevention and Control

text: public

text: sam_6F16A9CA-0A1E-4241-BE05-1B662602BDF2

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_492CAA42-411E-46A2-B67D-92083AB67D20

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_52F1B639-056B-4467-B88F-699827CBBF72

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_81216522-E6F0-4A1C-BB76-C199D6FF8156

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_DCF69A95-B09C-43D9-9003-2EB84F699F95

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_0F179C73-FA8C-4F1A-A440-6917BAA6EE92

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_A7BDA04D-F545-4E4E-A883-85D594E701E1

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_A5F70DAD-8552-4562-9B3F-3D8CA2648252

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

text: sam_3EB2F13A-477B-4EE3-AC11-38209850FA02

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_23A29105-9582-4424-8131-6345E073446E

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_6D5CEA91-F0F1-443B-AE05-A9AC50BF63E7

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_2C324038-F17C-464F-A36C-BBD6E442BF90

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_E00F6BDE-9C18-45A7-8480-D40AE907CAD0

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_5BC1E198-7014-479A-8C98-77EA95081077

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

text: sam_8A513E0B-3023-4308-8479-C33E04B16492

characteristic: Submitter Id

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: title


characteristic: ENA checklist

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: public

text: sam_F562AE3C-09F1-4FEF-BFB4-AEA33B0834F3

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: European Centre for Disease Prevention and Control

text: public

text: sam_B56864B9-2BC1-4485-971B-A3F7C6CE68E0

text: Slovenia

characteristic: collected by

characteristic: collection date

text: Slovenia

characteristic: country

text: yes

characteristic: host associated

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

text: sam_6B34231D-C81E-4882-B0C7-D56B37A76D11

text: Slovenia

text: Slovenia

text: yes

text: diseased

characteristic: host disease status

characteristic: isolate

text: Listeria monocytogenes

characteristic: organism

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens

characteristic: specific host


characteristic: ENA-LAST-UPDATE

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: sam_E801BE16-0819-4EC3-8345-0906FBDE2E61

text: Slovenia

text: Slovenia

text: yes

text: diseased

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Listeria monocytogenes

text: Homo sapiens


text: public

characteristic: INSDC status

characteristic: SRA accession

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

characteristic: Submitter Id

text: MGRAST

characteristic: broker name

characteristic: collection time

text: H2 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Microbial community in A2O or A2O-MBR

characteristic: project name

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method

text: H2 Taxonomy ID:256318

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

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text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: Q1 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

text: mimarks-survey

text: metagenome

characteristic: organism

text: Microbial community in A2O or A2O-MBR

characteristic: project name

text: metagenome

text: illumina

text: Q1 Taxonomy ID:256318

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: S_I Taxonomy ID:256318

text: terrestrial biome

text: organic feature

text: sludge

text: wastewater|sludge

text: China

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: mgrast id

text: metagenome

text: Microbial community in A2O or A2O-MBR

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method

text: S_I Taxonomy ID:256318

text: wastewater/sludge


text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: E4 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Microbial community in A2O or A2O-MBR

text: metagenome

text: illumina

text: E4 Taxonomy ID:256318

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: S_E Taxonomy ID:256318

text: terrestrial biome

text: organic feature

text: sludge

text: wastewater|sludge

text: China

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: mgrast id

text: metagenome

characteristic: organism

text: Microbial community in A2O or A2O-MBR

characteristic: project name

text: metagenome

text: illumina

text: S_E Taxonomy ID:256318

text: wastewater/sludge


text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: F_H Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

text: mimarks-survey

characteristic: investigation type

text: metagenome

text: Microbial community in A2O or A2O-MBR

characteristic: sample name

text: metagenome

text: illumina

characteristic: sequencing method

text: F_H Taxonomy ID:256318

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: MGRAST

text: S_Y Taxonomy ID:256318

text: terrestrial biome

text: organic feature

text: sludge

text: wastewater|sludge

text: China

text: Beijing

characteristic: geographic location (region and locality)

text: mimarks-survey

characteristic: mgrast id

text: metagenome

text: Microbial community in A2O or A2O-MBR

text: metagenome

text: illumina

text: S_Y Taxonomy ID:256318

characteristic: title

text: wastewater/sludge

characteristic: wastewater/sludge environmental package


text: public

text: MGRAST

characteristic: broker name

characteristic: collection date

characteristic: collection time

text: E1 Taxonomy ID:256318

characteristic: description

text: terrestrial biome

characteristic: environment (biome)

text: organic feature

characteristic: environment (feature)

text: sludge

characteristic: environment (material)

text: wastewater|sludge

characteristic: environmental package

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Beijing

text: mimarks-survey

characteristic: investigation type

text: metagenome

characteristic: organism

text: Microbial community in A2O or A2O-MBR

characteristic: project name

text: metagenome

text: illumina

text: E1 Taxonomy ID:256318

text: wastewater/sludge


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BANGOR UNIVERSITY, MEFGL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:BANGOR UNIVERSITY, MEFGL

characteristic: Submitter Id

text: Ephemera danica

text: Ephemera danica


text: BANGOR UNIVERSITY, MEFGL

text: public

characteristic: description

text: Notonecta glauca

text: Notonecta glauca

characteristic: title


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Bithynia tentaculata

text: Bithynia tentaculata


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Gyrinus marinus

text: Gyrinus marinus


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Asellus aquaticus

text: Asellus aquaticus


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Gammarus pulex

text: Gammarus pulex


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Bathyomphalus contortus

text: Bathyomphalus contortus


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Radix balthica

text: Radix balthica


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Physa fontinalis

text: Physa fontinalis


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Planorbis planorbis

text: Planorbis planorbis


text: BANGOR UNIVERSITY, MEFGL

text: public

text: Potamopyrgus antipodarum

text: Potamopyrgus antipodarum


text: UNIVERSITY OF NOTTINGHAM

text: public

tag: Namespace:UNIVERSITY OF NOTTINGHAM

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: Poultry

characteristic: host scientific name

text: J62 Flac Tn3

characteristic: isolate

text: Poultry

characteristic: isolation source

text: Escherichia coli

text: Escherichia coli

text: Escherichia coli J62 FlacTn3


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF NOTTINGHAM

text: public

text: Mutant of Escherichia coli J62 Flac Tn3

text: United Kingdom

text: diseased

text: Poultry

text: J62 Flac Tn3

text: Poultry

text: Escherichia coli

characteristic: organism

text: Escherichia coli

text: mutant 4

characteristic: strain

text: Escherichia coli J62 Flac Tn3


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SAHMRI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

characteristic: common name

text: Sputum

characteristic: environment (biome)

text: Sputum

characteristic: environment (feature)

text: Sputum

characteristic: environment (material)

text: Australia

text: 151.78 E

characteristic: geographic location (latitude)

text: 32.92 S

characteristic: geographic location (longitude)

text: human-oral

characteristic: human oral environmental package

text: metagenome

characteristic: investigation type

text: Homo sapiens

text: AMAZES

characteristic: project name

text: Homo sapiens

text: Illumina Miseq

characteristic: sequencing method

text: AMAZES sputum 16s


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UNIVERSITY OF TASMANIA

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF TASMANIA

characteristic: Submitter Id

characteristic: collection date

text: The spread of vancomycin-resistant Enterococcus faecium (VREfm) has become a challenge to healthcare infection control worldwide. In 2015, a marked increase in vancomycin-resistant Enterococcus faecium (VREfm) isolation was detected in public hospitals in Tasmania. We report here the draft whole genome sequence of a newly-designated VREfm sequence type isolate, ST1421.

characteristic: description

text: Australia

characteristic: geographic location (country and/or sea)

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Hospital Patient

characteristic: isolation source

text: Enterococcus faecium

text: Enterococcus faecium

text: Draft genome sequence of a new sequence type, ST1421, of Vancomycin-Resistant Enterococcus faecium (VREfm)

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:Max Planck Institue for Developmental Biology

text: Pristionchus pacificus

characteristic: organism

text: Pristionchus pacificus


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Max Planck Institue for Developmental Biology

characteristic: INSDC last update

text: public

text: Pristionchus pacificus

text: Pristionchus pacificus


text: Friedrich-Loeffler-Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Friedrich-Loeffler-Institute

characteristic: collecting institution

text: Laura Zani

characteristic: collector name

text: Deletion at the 5’-end of Estonian ASFV strains associated with an attenuated phenotype

text: Estonia

text: wild boar

characteristic: host common name

text: diseased

text: Sus scrofa scrofa

text: female

characteristic: host sex

characteristic: host subject id

text: Estonia 2014

text: African swine fever virus

text: African swine fever virus

text: Estonia 2014


AD-CAI

text: HUJI

text: public

text: AD-CAI

characteristic: collection date

text: Whole-genome shotgun sequencing of Aleurodicus dispersus whole genome amplified bacteriome enriched samples

characteristic: description

text: Spain

characteristic: geographic location (country and/or sea)

text: Canary Islands

characteristic: geographic location (region and locality)

text: Estrella Hernandez-Suarez

characteristic: identified by

text: Aleurodicus dispersus

text: Aleurodicus dispersus

text: Bacteriomes

characteristic: tissue type

text: Aleurodicus dispersus bacteriomes whole-genome shotgun

characteristic: title


AF-CAI

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: HUJI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: AF-CAI

text: Whole-genome shotgun sequencing of Aleurodicus floccissimus whole genome amplified bacteriome enriched samples

text: Spain

text: Canary Islands

text: Estrella Hernandez-Suarez

text: Aleurodicus floccissimus

characteristic: organism

text: Aleurodicus floccissimus

text: Bacteriomes

text: Aleurodicus floccissimus bacteriomes whole-genome shotgun


TV-BCN

text: HUJI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TV-BCN

characteristic: Submitter Id

text: greenhouse whitefly

characteristic: common name

text: Whole-genome shotgun sequencing of Trialeurodes vaporariorum whole genome amplified bacteriome enriched samples

text: Spain

text: Barcelona

text: Francisco Jose Beitia

text: Trialeurodes vaporariorum

text: Trialeurodes vaporariorum

text: Bacteriomes

text: Trialeurodes vaporariorum bacteriomes whole-genome shotgun


text: Mus musculus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: subject id


text: WT

characteristic: ArrayExpress-PHENOTYPE

text: Homo sapiens

text: SC

text: public

text: human

text: Homo sapiens

text: WT

characteristic: phenotype

text: Homo sapiens

text: Home sapiens


Trichococcus ART11

text: WAGENINGEN UNIVERSITY

text: public

text: Trichococcus ART11

tag: Namespace:WAGENINGEN UNIVERSITY

text: Trichococcus sp. ART1

text: Trichococcus sp. ART1

text: Genomic assembly of the psychrotolerant bacterium, Trichococcus ART1

characteristic: title


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES

characteristic: collection date

text: Norway spruce

characteristic: estimated size

text: Sweden

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Picea abies

text: Norway spruce

characteristic: organism common name

text: dry seed

characteristic: plant developmental stage

text: seed

characteristic: plant structure

characteristic: ploidy

text: Picea abies

characteristic: source material identifiers


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Norway spruce

characteristic: common name

text: Sweden

text: Picea abies

characteristic: organism

text: Norway spruce

text: dry seed

text: seed

text: Picea abies


text: Klebsiella pneumoniae

characteristic: ArrayExpress-SPECIES

characteristic: ENA-CHECKLIST

text: SC

text: public

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

characteristic: subject id

text: Klebsiella pneumoniae

characteristic: title


text: public

tag: Namespace:Center for Innovative Medicine & Department for Biosciences and Nutrition, Karolinska Institutet

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Wild type C57BL/6 female mice aged 9 weeks were each subjected to one 3 mm punch biopsy and sacrificed at given time points (2, 6 or 24 hours). The skin was harvested from the area of the wound and placed in RNA-later (Qiagen). Approximately 1-1.5 mm of skin, lining the wound edge, was cut out under a dissection microscope (Zeiss Discovery v20) using forceps and scissors, chopped into fine pieces and used for RNA isolation. The skin from the initial punch biopsy was taken as a control. The NEBNext Ultra Directional RNA library Prep kit (NEB) was used for preparing the samples for RNA-seq together with the NEBNext Poly(A) mRNA magnetic isolation module (NEB) according to manufacturers instructions. 1-2 µg of total RNA was used as starting material. For library preparation, adapters and index primers from the NEBNext Multiplex Oligos for Illumina kit were used.

characteristic: description

text: wild type genotype

characteristic: genotype

characteristic: individual

text: 3 millimetre cutaneous wound

characteristic: injury

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: wound edge

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Center for Innovative Medicine & Department for Biosciences and Nutrition, Karolinska Institutet

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

text: wild type genotype

text: 3 millimetre cutaneous wound

text: Mus musculus

text: Mus musculus

text: dorsal skin

text: wound edge

text: Mus musculus

text: female


characteristic: ENA-CHECKLIST

text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: house mouse

characteristic: common name

characteristic: description

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: dorsal skin

text: dorsal skin

text: Mus musculus

text: female

characteristic: title


E-MTAB-6686:ctrl 3

text: public

text: E-MTAB-6686:ctrl 3

text: ArrayExpress

text: house mouse

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: dorsal skin

characteristic: organism part

text: dorsal skin

characteristic: sampling site

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

text: ctrl 3


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

tag: Namespace:University of Freiburg Institute for Biology I (Zoology) Evolutionary Biology & Ecology

text: less than 1

unit: year

text: ArrayExpress

text: Protocols: Heads were flushed with RNAlater™ (Qiagen) to ensure complete permeation of the head tissue. The samples were transported on ice to the field station and kept overnight at 4 °C to ensure full permeation. Then samples were kept frozen in a -20 °C fridge not more than two weeks. During transport, the samples were kept in an insulated container, cooled on ice, until arrival in the laboratory in Freiburg (Germany). There, samples were kept in a -80 °C freezer until further processing. Total RNA was extracted from the head of single individuals according to a modified version of the peqGOLD TriFast™ protocol: modifications were an incubation time of 10 min instead of 5 min at room temperature after adding 900 μl peqGOLD Tri Fast™ and inverting the tube. After adding chloroform and after incubation, centrifugation was modified to 10 min at 4 °C, 10,800 rpm. After transfer of the aqueous phase into a new Eppendorf tube, we added another centrifugation step for 5 min at 4 °C (10,800 rpm). Then the supernatant was transferred into a new Eppendorf tube and 2 μl nuclease free glycogen (5 mg/ml) was added per sample. After adding isopropanol, the mixture was incubated for 10 min at room temperature and not on ice. After washing the RNA pellet with 75% ethanol and vortexing, the sample was centrifuged for 5 min at 4 °C, 8,500 rpm. This step was repeated three times. After dissolving the pellet in nuclease-free water, samples were kept for at least one hour at 4 °C. DNA digestion was performed using DNase I Amplification Grade Kit (Sigma-Aldrich). The concentration and quality of the isolated RNA was checked with an Agilent Bioanalyzer (Agilent RNA 6000 Nano Kit). Library preparation was done by BGI. Libraries were constructed with the Ribo-Zero® rRNA Removal Kit (Human/Mouse/Rat), Illumina (http://www.illumina.com/products/ribo-zero-rrna-removal-human-mouse-rat.html).

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: king

characteristic: phenotype

text: Africa, Cote d'Ivoire, Comoe National Park, Coordinates 8.6550568, -3.7823524 +- 1 km, 200m

text: Macrotermes bellicosus

text: male


tag: attribute

characteristic: ENA-CHECKLIST

text: University of Freiburg Institute for Biology I (Zoology) Evolutionary Biology & Ecology

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: less than 1

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: king

text: Macrotermes bellicosus

text: male


text: public

text: less than 6

text: ArrayExpress

characteristic: description

text: Macrotermes bellicosus

characteristic: organism

text: Macrotermes bellicosus

text: head

characteristic: organism part

text: king

text: Macrotermes bellicosus

text: male

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: public

unit: month

text: ArrayExpress

text: Macrotermes bellicosus

text: Macrotermes bellicosus

text: head

text: major worker

characteristic: sampling site

text: Macrotermes bellicosus