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tag: Namespace:VTT Technical Research Centre of Finland Ltd

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text: deep subsurface

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text: Outokumpu

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text: Staphylococci causing neonatal sepsis in LMIC Saureus & CoNs

text: No

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text: Bangladesh

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text: No

text: Ethiopia

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text: Staphylococcus aureus

text: Staphylococcus aureus


text: CARDIFF UNIVERSITY

text: CARDIFF UNIVERSITY

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characteristic: collection date

text: No

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text: Nigeria

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characteristic: is the sequenced pathogen host associated?

text: Staphylococcus aureus

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text: No

text: South Africa

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text: Yes

text: Staphylococcus aureus

text: Staphylococcus aureus


text: CARDIFF UNIVERSITY

text: CARDIFF UNIVERSITY

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text: research nurses

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characteristic: collection date

text: No

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text: Bangladesh

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text: diseased

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text: human

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text: Yes

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text: Staphylococcus sciuri

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text: Staphylococcus sciuri


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text: CARDIFF UNIVERSITY

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text: No

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characteristic: geographic location (latitude)

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text: Staphylococcus aureus

text: Staphylococcus sciuri

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text: No

text: Pakistan

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text: Yes

text: Staphylococcus aureus

text: Staphylococcus sciuri


text: CARDIFF UNIVERSITY

text: CARDIFF UNIVERSITY

text: public

text: research nurses

characteristic: collected by

characteristic: collection date

text: No

characteristic: environmental sample

text: Nigeria

characteristic: geographic location (longitude)

text: diseased

characteristic: host health state

text: human

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text: Yes

characteristic: is the sequenced pathogen host associated?

text: Staphylococcus haemolyticus

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text: Staphylococcus haemolyticus


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characteristic: ENA-CHECKLIST

characteristic: External Id

text: CARDIFF UNIVERSITY

text: CARDIFF UNIVERSITY

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text: research nurses

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text: No

text: Nigeria

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

text: diseased

text: human

text: Yes

text: Staphylococcus epidermidis

text: Staphylococcus epidermidis

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characteristic: title


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text: University Hospital Galway

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text: University Hospital Galway

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text: public

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text: sam_NSSLRL_193b3fe6-f113-4a61-8ce4-4dc73fa674e9

tag: Namespace:University Hospital Galway

characteristic: Submitter Id

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text: Salmonella enterica

text: Salmonella enterica subsp. enterica serovar Kentucky


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text: GENOME INSTITUTE OF SINGAPORE

text: GENOME INSTITUTE OF SINGAPORE

text: public

tag: Namespace:GENOME INSTITUTE OF SINGAPORE

text: human

characteristic: common name

text: Homo sapiens


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text: public

tag: Namespace:NEIKER-Instituto Vasco de Investigacion y Desarrollo Agrario

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text: Soil metagenome

text: agricultural field

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text: Spain

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text: metagenome

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text: soil metagenome

text: Uragan

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text: Soil metagenome


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text: NEIKER-Instituto Vasco de Investigacion y Desarrollo Agrario

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characteristic: INSDC center name

text: public

text: soil metagenome

text: agricultural field

text: Spain

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characteristic: geographic location (latitude)

text: metagenome

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text: Uragan

text: amplicon

text: soil metagenome

characteristic: title


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text: public

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tag: Namespace:Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany

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unit: week

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text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Colon tissues were harvested from euthanized mice. The rectal tissues were discarded and 0.2 to 0.3 cm of the distal colon was collected in RNA later solution and immediately snap frozen in liquid nitrogen. 10 week old mice were challenged with 3% DSS in drinking water. Mice were divided into two groups, one received sterile PBS as control and the other received 1mg.kg-1 of EP4-D dissolved in sterile PBS once daily via oral gavage. The volume of gavage was set such that desired dosage was achieved by gavaging (body weight in grams X 10) in microliters. For e.g a 20g mouse received an oral bolus of 200 microliters* (either vehicle or compound) Total tissue RNA was extracted using the column based RNA extraction kit, Total RNA Kit, peqGOLD (VWR GmbH, Munich, Germany) as per manufacturer's instructions. From the RNA sample to the final data, each step, including sample test, library preparation, and sequencing, influences the quality of the data, and data quality directly impacts the analysis results. To guarantee the reliability of the data, quality control (QC) is performed at each step of the procedure. After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies). Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

characteristic: description

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text: Mus musculus

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text: male

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text: Department of Medicine 1, University of Erlangen-Nuremberg, Erlangen, Germany

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text: ArrayExpress

text: house mouse

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text: Mus musculus

text: colon

text: male


characteristic: ENA first public

text: WWU

text: (Westphalian Wilhelms) University of Muenster, Germany

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text: public

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characteristic: collection date

characteristic: couple

text: animal cage

characteristic: environment (biome)

text: nest of bird

characteristic: environment (feature)

text: endodermal part of digestive tract

characteristic: environment (material)

text: Germany

characteristic: geographic location (country and/or sea)

text: 52°02'9.60 N

characteristic: geographic location (latitude)

text: 8°29'20.99 E

characteristic: geographic location (longitude)

text: Feces

characteristic: host body site

text: Taeniopygia guttata

characteristic: host common name

text: Father

characteristic: host family relationship

text: male

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text: host-associated

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text: bird metagenome

characteristic: organism

text: forward 5′-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3′ reverse 5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3′

characteristic: pcr primers

characteristic: project name

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text: MiSeq

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text: 16S rRNA

characteristic: target gene

characteristic: target subfragment

text: Gut microbial community of two estrildid finch species, the Bengalese finch (Lonchura striata domestica) and the zebra finch (Taeniopygia guttata)

characteristic: title


characteristic: ENA first public

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characteristic: External Id

text: University of Southampton

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text: University of Southampton

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text: public

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tag: Namespace:University of Southampton

characteristic: Submitter Id

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text: COI Control 1

characteristic: description

text: marine benthic

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text: submarine canyon

characteristic: environment (feature)

text: sediment

characteristic: environment (material)

text: Mediterranean Sea

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq


characteristic: ENA first public

characteristic: ENA last update

characteristic: ENA-CHECKLIST

characteristic: External Id

text: University of Southampton

characteristic: INSDC center alias

text: University of Southampton

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text: COI Control 2

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text: submarine canyon

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text: metagenome

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text: metagenome

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text: Illumina MiSeq

characteristic: sequencing method

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text: University of Southampton

text: University of Southampton

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text: COI Control 3

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text: submarine canyon

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text: sediment

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text: Mediterranean Sea

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text: metagenome

text: metagenome

text: sediment

text: Illumina MiSeq


characteristic: ENA first public

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text: University of Southampton

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text: University of Southampton

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text: Mediterranean Sea

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: metagenome

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text: Illumina MiSeq


text: University of Southampton

text: University of Southampton

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text: marine benthic

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text: Illumina MiSeq

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characteristic: External Id

text: University of Southampton

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text: University of Southampton

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text: COI Control 6

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text: sediment

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text: Mediterranean Sea

characteristic: geographic location (country and/or sea)

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text: metagenome

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text: Illumina MiSeq


text: University of Southampton

text: University of Southampton

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text: COI Control 7

text: marine benthic

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text: Mediterranean Sea

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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text: Illumina MiSeq


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characteristic: External Id

text: University of Southampton

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text: University of Southampton

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text: COI Palermo Pristine Arenella 1

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text: University of Southampton

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text: COI Palermo Pristine Arenella 2

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text: Mediterranean Sea

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text: metagenome

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text: Illumina MiSeq


characteristic: ENA first public

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text: University of Southampton

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text: University of Southampton

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text: COI Palermo Pristine Arenella 3

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text: Mediterranean Sea

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

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text: metagenome

text: sediment

characteristic: sediment environmental package

text: Illumina MiSeq


text: University of Southampton

text: University of Southampton

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text: COI Palermo Pristine Eleuterio 1

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characteristic: sequencing method

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text: University of Southampton

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text: University of Southampton

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characteristic: geographic location (country and/or sea)

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text: University of Southampton

text: University of Southampton

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characteristic: geographic location (depth)

characteristic: geographic location (elevation)

characteristic: geographic location (latitude)

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text: University of Southampton

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text: University of Southampton

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text: COI Castellmare Impacted 1

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text: Mediterranean Sea

text: metagenome

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characteristic: sequencing method

characteristic: title


text: University of Southampton

text: University of Southampton

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