characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: INSTITUT PASTEUR

text: public

text: sequence type 17

text: France

text: Human

text: Urine

text: Streptococcus agalactiae

text: Streptococcus agalactiae


E-MTAB-2947:Sample 2

status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-2947:Sample 2

tag: Namespace:Universite Lyon 1 -CNRS - UMR5240 Microbiologie Adaptation Pathogenie

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: Bacteria were grown with shaking (150 rpm) at 28 degrees C in YPG media (5 g/L yeast extract; 5 g/L peptone; 10 g/L glucose; pH 7.2), in AT minimal media (80 mM KH2PO4; 0.65 mM MgSO4, 7H2O; 18 uM FeSO4, 7H2O; 70 uM CaCl2, 2H2O; MnCl2, 10 uM 4H2O; pH 7.2) supplemented with 10 mM succinate as carbon source and 10 mM ammonium sulfate as nitrogen source (Petit, Tempe et al. 1978). Total RNAs were extracted as previously described (Hommais, Oger-Desfeux et al. 2008) and DNA contamination was eliminated with a DNase I treatment (Roche). 100 ug of total RNAs were separated on a 15 % denaturing polyacrylamide gel (7M urea, 1X TBE) and RNAs with size ranging from 25 to 500 nt were extracted. Rapidly, piece of gel containing RNAs was broken mechanically and incubated 4 h in 500 ul of 10 mM Tris-HCl, 1 mM EDTA, 300 mM NaCl buffer with soft shaking at 15 degrees C. Size-selected RNAs were twice filtrated and ethanol precipitated. 5S RNA and tRNAs depletions were performed from 2.5 ug of size-selected RNAs by reverse transcription treatment using First strand cDNA synthesis kit (Life biosciences) with 100 ng of primer 5S and 50 ng of each other primer representing tRNAs (Table S2). A RNAse H treatment was then performed and newly synthesized DNAs were eliminated with a DNAse I treatment (DNA-free kit, Ambion). The library preparation was an adaptation of the Illumina directional mRNA-Seq protocol, using the DGE-Small RNA sample preparation kit. 200 ng of selected small RNAs were treated by Antarctic Phosphatase (NEB, cat.#M0289S) and T4 PolyNucleotide Kinase (NEB, cat.#M0201S) and purified on RNeasy MinElute spin column (Qiagen, cat.#74204). Ligations with Illumina v1.5 sRNA 3' adapter and sRNA 5' adapter, reverse transcription, PCR amplification and purification with Agencourt AMPure beads (Beckman, A63880) were performed as described in the Illumina directional mRNA-Seq protocol from Illumina.

characteristic: description

text: YPG medium (rich)

characteristic: growth condition

text: exponential

characteristic: growth phase

text: Agrobacterium tumefaciens str. C58

characteristic: organism

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

characteristic: strain

text: Sample 2

characteristic: title


E-MTAB-2947:Sample 7

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text: Universite Lyon 1 -CNRS - UMR5240 Microbiologie Adaptation Pathogenie

text: public

text: E-MTAB-2947:Sample 7

text: ArrayExpress

text: AT medium (minimal)

text: stationary

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 7


E-MTAB-2947:Sample 4

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-2947:Sample 4

text: ArrayExpress

text: YPG medium (rich)

text: stationary

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 4


E-MTAB-2947:Sample 5

characteristic: ENA-CHECKLIST

text: public

text: E-MTAB-2947:Sample 5

text: ArrayExpress

text: AT medium (minimal)

text: exponential

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 5


E-MTAB-2947:Sample 8

characteristic: External Id

text: public

text: E-MTAB-2947:Sample 8

text: ArrayExpress

text: AT medium (minimal)

text: stationary

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 8


E-MTAB-2947:Sample 1

characteristic: INSDC center name

text: public

text: E-MTAB-2947:Sample 1

text: ArrayExpress

text: YPG medium (rich)

text: exponential

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 1


E-MTAB-2947:Sample 6

characteristic: INSDC first public

text: public

text: E-MTAB-2947:Sample 6

text: ArrayExpress

text: AT medium (minimal)

text: exponential

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 6


E-MTAB-2947:Sample 3

characteristic: INSDC last update

text: public

text: E-MTAB-2947:Sample 3

text: ArrayExpress

text: YPG medium (rich)

text: stationary

text: Agrobacterium tumefaciens str. C58

text: Agrobacterium fabrum str. C58

text: Agrobacterium fabrum str. C58

text: Sample 3


text: 33347430; 34414415; 34461978; 35780211

text: CTB/NICD

text: public

characteristic: INSDC status

text: ZAF

text: NDM Oxford

text: Mycobacterium

characteristic: genus

characteristic: isolate

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: SAPA00082962_S7. CTB/NICD. PA00082962_S7

type: AMR curated data - CABBAGE

value: rifampin

value: resistant

value: Mycobacterium tuberculosis

value: pyrazinamide

value: susceptible

value: isoniazid

value: ethambutol


text: 34414415; 34461978; 35780211

text: CTB/NICD

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text: ZAF

characteristic: SRA accession

characteristic: Submitter Id

text: NDM Oxford

characteristic: broker name

text: Mycobacterium

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: SAEI00622581_S5. CTB/NICD. EI00622581_S5


text: 33347430; 34414415; 34461978; 35780211

text: CTB/NICD

text: public

text: ZAF

text: NDM Oxford

text: Mycobacterium

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: SATRL0074347_S14. CTB/NICD. TRL0074347_S14


text: unidentified

characteristic: ArrayExpress-Species

text: SC

text: public

text: unidentified

text: unidentified


text: Mycobacterium tuberculosis

text: Thailand

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

text: Thailand

text: SC

text: public

text: THA

text: Mycobacterium

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand

characteristic: strain

value: streptomycin


text: Mycobacterium tuberculosis

text: Thailand

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text: SC

text: public

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text: Mycobacterium

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

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text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

text: Thailand

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text: SC

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text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

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text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

text: Thailand

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text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


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text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

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text: Mycobacterium tuberculosis

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text: THA

text: Mycobacterium

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

text: Thailand

text: SC

text: public

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text: Mycobacterium

characteristic: genus

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Thailand


text: Mycobacterium tuberculosis

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text: Mycobacterium

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text: Mycobacterium tuberculosis

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characteristic: Submitter Id

text: Mycobacterium

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text: Plant:tobacco plant

characteristic: specific host

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Pseudomonas aeruginosa

characteristic: common name

text: UK

text: not available: not collected

text: not available: not collected

text: Pseudomonas aeruginosa

characteristic: organism

text: Pseudomonas aeruginosa

text: not available

characteristic: serovar

text: Human


characteristic: ENA-CHECKLIST

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: Pseudomonas aeruginosa

text: Infection

text: Ear

text: Pseudomonas aeruginosa

text: Pseudomonas aeruginosa

text: not available

text: not available

characteristic: strain


sample_AMX_312236_Tipula oleacera

text: GSC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: sample_AMX_312236_Tipula oleacera

text: Tipula oleracea

text: Tipula oleracea


text: Chlamydia pecorum

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: Chlamydia pecorum

characteristic: sample description

text: Chlamydia pecorum


text: Chlamydia pecorum

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Chlamydia pecorum

text: QLD/Bobby/Eye

text: Chlamydia pecorum


text: Chlamydia pecorum

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Chlamydia pecorum

text: QLD/Bobby/UGT

text: Chlamydia pecorum


text: Chlamydia pecorum

text: SC

text: public

text: Chlamydia pecorum

text: QLD/Hume/Penile

text: Chlamydia pecorum


text: Chlamydia pecorum

text: SC

text: public

text: Chlamydia pecorum

text: NSW/Dobby/Penile

text: Chlamydia pecorum


text: Chlamydia pecorum

text: SC

text: public

text: Chlamydia pecorum

text: QLD/Heri/Eyes

text: Chlamydia pecorum


text: Mycobacterium tuberculosis

text: SC

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: UB

text: public

text: DNA sample prepared for Nanopore sequence run

characteristic: description

unit: MB

characteristic: estimated size

text: Invisorb Spin Cell Mini Kit (Invitek, Birkenfeld, Germany), following manufacturers protocol for extraction from serum and plasma.

text: Escherichia coli str. K-12 substr. MG1655

text: L-shaped spreader

text: MinION (Oxford Nanopore Technologies), R7 chemistry

characteristic: seq meth

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: External Id

text: Uppsala University

text: public

tag: Namespace:Uppsala  University

text: Sampled in Uppsala

text: Ficedula hypoleuca

characteristic: organism

text: Ficedula hypoleuca

text: Male

characteristic: sex


text: Uppsala University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Sampled in Uppsala

text: Ficedula hypoleuca

text: Ficedula hypoleuca

text: Female


text: unidentified

characteristic: ArrayExpress-Species

text: SC

text: public

characteristic: INSDC status

text: unidentified

text: unidentified


UAM-MAO

characteristic: ENA-FIRST-PUBLIC

text: public

text: UAM-MAO

text: Chrysosporum ovalisporum

text: Chrysosporum ovalisporum

text: UAM-MAO

characteristic: strain

text: Aphanizomenon ovalisporum UAM-MAO


text: Influenza A virus

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: SRA accession

text: Influenza A virus

text: Influenza A virus


text: Streptococcus pneumoniae

text: SC

text: public

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae


text: Mycobacterium africanum

text: SC

text: public

text: Mycobacterium africanum

text: Mycobacterium africanum


text: Salmonella enterica subsp. enterica serovar Typhimurium

text: SC

text: public


text: unidentified virus

text: SC

text: public

text: unidentified virus

text: unidentified virus


text: Influenza B virus

text: SC

text: public

text: Influenza B virus

text: Influenza B virus


text: Escherichia coli

text: SC

text: public

text: Escherichia coli

text: Escherichia coli


text: SC

text: public

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae


text: Leishmania donovani

text: SC

text: public

text: Leishmania donovani

text: Leishmania donovani


text: SC

text: public

text: USA

characteristic: anonymized name

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Bacteremia

characteristic: host status

characteristic: isolate

text: Blood

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain

value: CLSI

value: broth dilution

value: mg/L


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Pneumonia

text: Blood

text: blood

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title

value: resistant


characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: USA

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Pneumonia

text: Blood

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human

value: susceptible


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

text: public

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Bacteremia

characteristic: host status

characteristic: isolate

text: Blood

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain


characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: USA

characteristic: SRA accession

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Bacteremia

text: Blood

text: blood

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: USA

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Pneumonia

text: Blood

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Pneumonia

characteristic: host status

characteristic: isolate

text: Blood

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: USA

characteristic: SRA accession

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Bacteremia

text: Blood

text: blood

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: USA

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Bacteremia

text: Blood

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: Pneumonia

characteristic: host status

characteristic: isolate

text: BLOOD

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain

characteristic: taxon id


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: USA

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: meningitis

text: BLOOD

text: blood

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

text: USA

characteristic: anonymized name

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: bacteremia

characteristic: host status

text: BLOOD

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: meningitis

characteristic: isolate

text: BLOOD

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain

characteristic: taxon id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: USA

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: bacteremia

text: BLOOD

text: blood

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: USA

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: Pneumonia

characteristic: host status

text: BLOOD

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: USA

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: bacteremia

characteristic: isolate

text: BLOOD

characteristic: isolation source

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host

characteristic: sub strain


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC first public

text: public

text: USA

characteristic: SRA accession

characteristic: Submitter Id

characteristic: anonymized name

text: Streptococcus pneumoniae

text: USA

text: Streptococcus

text: Homo sapiens

text: meningitis

text: CSF

text: central nervous system

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Human

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC last update

text: public

text: USA

characteristic: collection date

text: Streptococcus pneumoniae

characteristic: common name

text: USA

characteristic: country

text: Streptococcus

characteristic: genus

text: Homo sapiens

characteristic: host

text: bacteremia

characteristic: host status

text: BLOOD

text: blood

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: Human