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characteristic: host disease status

characteristic: host subject id

text: intestine environment

text: TAAGGCGA-TCCTTACG

text: human gut metagenome

text: MARS Fecal Nextera Shotgun Sequencing

text: human gut metagenome

text: Illumina NovaSeq 6000

text: gut metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: CGS-GL

characteristic: INSDC first public

text: public

text: digestive tract environment

text: fecal sample

text: organic matter

text: USA

text: gut

text: Asthmatic

text: intestine environment

characteristic: local environmental context

text: TAAGGCGA-ACGCGTGG

characteristic: multiplex identifiers

text: human gut metagenome

characteristic: organism

text: MARS Fecal Nextera Shotgun Sequencing

characteristic: project name

text: human gut metagenome

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: gut metagenome

characteristic: title


characteristic: External Id

text: CGS-GL

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: digestive tract environment

text: fecal sample

characteristic: description

text: organic matter

characteristic: environmental medium

text: USA

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: gut

characteristic: host body site

text: Asthmatic

text: intestine environment

text: TAAGGCGA-GGAACTCC

text: human gut metagenome

text: MARS Fecal Nextera Shotgun Sequencing

text: human gut metagenome

text: Illumina NovaSeq 6000

text: gut metagenome


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:German Center for Neurodegenerative Diseases (DZNE)

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: The brain samples and/or bio samples were obtained from the Netherlands Brain Bank, Netherlands Institute for Neuroscience, Amsterdam (open access: www.brainbank.nl). All Material has been collected from donors for or from whom a written informed consent for a brain autopsy and the use of the material and clinical information for research purposes had been obtained by the NBB. Additional samples were provided by the Queen Square Brain Bank of Neurological Disorders and MRC, King College London. We complied to all relevant regulations of the mentioned brain banks for the work with these samples. Total RNA for RNA-seq was isolated from ±100mg of frozen brain tissue with TRIzol reagent (Thermo Fischer Scientific) according to the manufacturer recommendation, followed by purification with the RNeasy mini columns (Qiagen) after DNAse treatment. Total RNA-seq libraries were prepared from 1 microgram of total RNA from frozen brain tissue using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina) according to the protocol specifications.

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: External Id

text: German Center for Neurodegenerative Diseases (DZNE)

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: description

text: adult

text: normal

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: human

text: adult

text: normal

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: female


text: public

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: frontotemporal dementia

characteristic: disease

text: C9orf72 mutation

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: male


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

text: frontotemporal dementia

text: C9orf72 mutation

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

characteristic: description

text: adult

text: frontotemporal dementia

text: GRN mutation

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: frontotemporal dementia

text: GRN mutation

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: male


characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: human

characteristic: common name

text: adult

characteristic: developmental stage

text: frontotemporal dementia

characteristic: disease

text: MAPT mutation

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: adult

text: frontotemporal dementia

text: MAPT mutation

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: frontal lobe

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

text: DEPT OF MICROBIOLOGY

characteristic: INSDC first public

text: public

characteristic: INSDC status

tag: Namespace:DEPT OF MICROBIOLOGY

characteristic: collection date

text: Klebsiella pneumoniae B2562/19-Greece

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: homo sapiens

characteristic: host scientific name

characteristic: isolate

text: urine

text: not provided

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

text: not provided

characteristic: serovar

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DEPT OF MICROBIOLOGY

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae B11395/18-Greece

text: Greece

text: diseased

text: homo sapiens

text: urine

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


characteristic: ENA-LAST-UPDATE

text: DEPT OF MICROBIOLOGY

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: collection date

text: Klebsiella pneumoniae C251/19-Greece

text: Greece

text: diseased

text: homo sapiens

text: rectal swab

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


text: DEPT OF MICROBIOLOGY

text: public

text: Klebsiella pneumoniae C746/19-Greece

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: diseased

characteristic: host health state

text: homo sapiens

characteristic: host scientific name

text: rectal swab

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


text: Pneumococcus

characteristic: ArrayExpress-SPECIES

text: SC

text: public

text: Pneumococcus

characteristic: common name

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

text: Strepcococcus pneumoniae


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: UMR 1137 IAME

text: public

tag: Namespace:UMR 1137 IAME

text: France

text: healthy

text: homo sapiens

text: Faeces

characteristic: isolate

text: viral metagenome

text: viral metagenome

characteristic: strain

characteristic: title


characteristic: External Id

text: Sorbonne University

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: SRA accession

tag: Namespace:Sorbonne University

characteristic: Submitter Id

text: Telomerase mutant LMJ.RY0402.077111

text: Chlamydomonas reinhardtii

text: Chlamydomonas reinhardtii


characteristic: ENA-LAST-UPDATE

text: Sorbonne University

characteristic: INSDC first public

text: public

characteristic: INSDC status

text: Long-term culture of CC-4533

characteristic: description

text: Chlamydomonas reinhardtii

text: Chlamydomonas reinhardtii


text: Sorbonne University

text: public

text: Telomerase mutant LMJ.RY0402.209904

text: Chlamydomonas reinhardtii

text: Chlamydomonas reinhardtii


text: Wellcome Sanger Institute

text: public

tag: Namespace:Wellcome Sanger Institute

text: ArrayExpress

characteristic: broker name

text: trophoblast cell

text: human

text: Protocols: This dataset profiles: A) human Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues(Okae, H. et al. 2018) and B) human primary trophoblast organoids grown and differentiated into EVT as previously described by Turco et al 2018 and Sheridan et al 2020. See details in the \growth protocol\ section below. Both organoids were dissociated for single-cell or single-nuclei RNA-sequencing using the following protocols. - Dissociation of human Trophoblast stem cell: For single-cell transcriptome analysis, TS/EVT cells were PBS washed and dissociated with TrypLE as above. TrypLE was neutralised with PBS supplemented with 10%nFBS instead and filtered through a 40um strainer (pluriSelect pluriStrainer Mini). Cells were pelleted and washed twice with 1mL of PBS supplemented with 0.04% BSA (WAKO) and resuspended in 100µL of the same PBS+BSA before counting with LunaFL. A total of 2,000-5,000 cells were loaded onto the 10x Genomics Chromium inlet. - Dissociation of primary trophoblast organoids (for EVT): Single-cell isolation from EVT organoids was performed as previously described (Sheridan et al 2020). In brief, EVT organoids were released from the ibidi dish with Cell Recovery Solution and washed with ice cold PBS. EVT organoids were dissociated with Stem Pro Accutase at 37C for 5min and 0.5 m/mL Collagenase V solution for 15 min. Single-cell suspension from EVT organoids was resuspended in 0.4%/BSA, filtered through a 40um strainer, stained with trypan blue and counted with a haemocytometer. Single cell suspensions were diluted to targeted final concentration to recover ~5000-10,000 cells per sample prior to loading prior to loading of the 10x Genomics Chromium inlet. - Nuclei of trophoblast organoids (primary and okae): Trophoblast organoids pellets were released from the culture plate as previously described (Sheridan et al 2020). In brief, 1.5ml of Cell Recovery Solution was added into the pellet to dissolve the Matrigel for 45 min on ice. Trophoblast organoids were collected by centrifugation at 600g for 6 min. Supernatant was removed and the pellet was resuspended in ice cold PBS. Trophoblast pellet was snap frozen for single nuclei isolation. Nuclei was released with the dounce homogenizer method as previously described (Krishnaswami SR et al 2016). Nuclei suspension was resuspended in PBS/1% BSA stained with trypan blue, counted with a haemocytometer and diluted to targeted final concentration to recover ~10,000 nuclei per sample prior to loading prior to loading of the 10x Genomics Chromium inlet. Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae, H. et al. 2018). In brief, TSC self-renewing medium (TSCM) components were substituted with local suppliers with the exception for 30% w/v BSA from WAKO Japan and CHIR99021 concentration was increased to 6 µM which maintained the undifferentiated morphology as well as preserving its EVT invasive morphology. TSCs were grown on 5 µg/mL Collagen IV (Corning) coated wells and early passaged cells between p24 to 26 were used for differentiation and analysis. For 2D differentiation into EVT identity, cells were seeded at a density of 1.3x105/cm2 (corresponding to 125,000 cells plated on a well of a 6-well plate) in EVT media 1 detailed below supplemented with ice-cold 2% Matrigel GFR (Corning) before seeding on 1 µg/mL Collagen IV (Corning) coated wells (D0). Three days later (D3), media was changed to EVT media 2 supplemented with ice-cold 0.5% Matrigel GFR. Three days later (D6), the media was changed to EVT media 3 supplemented with ice-cold 0.5% Matrigel GFR. Cells were TrypLE-treated for downstream analysis 48h later (D8). For CXCL16 induction experiments, a final concentration of 100ng/mL CXCL16 (RnD 976-CX-025 with carrier, dissolved in 0.1%BSA(WAKO)/PBS) were supplemented to EVT media 2 or 3 and analysed 48h later. The induction was controlled by supplementing an equal volume of 0.1%BSA/PBS. In total, six trophoblast organoids were grown and differentiated into EVT as previously described (Turco et al 2018; Sheridan et al 2020). To differentiate trophoblast organoids into EVT, organoids were cultured with trophoblast organoid media (TOM) for ~3-4 days and transferred into EVT media 1 (+NRG1) for ~4-7 days. Once trophoblasts initiate their commitment into EVT (spike emergence), EVT media 2 (-NRG1) is added for 4 days. Donors were differentiated and collected in batches of three that were multiplexed on the same 10x Genomics reaction. Samples for donors 1, 2 and 3 were collected at 3 hours (h), 24h and 48h after the addition of EVTM media 2, while samples for donors 4, 5 and 6 were collected at 48h before, and then 0h, 48h and 96h after, addition of EVTM media 2. Organoids grown in trophoblast organoid media (TOM) media were also collected as a control at 96h. Media compositions were described previously: TSCM = DMEM/F12 with Glutamax (Gibco) supplemented with 0.2% v/v FBS (Gibco), 0.3% w/v BSA (WAKO), 1% ITS-X (Gibco), 2.5 µg/mL L-ascorbic acid-2-phosphate (Sigma), 50 ng/mL EGF (Peprotech AF-100-15), 6 µM CHIR99021 (Tocris 4423), 0.5 µM A83-01 (Tocris 2939), 1 µM SB43154 (Tocris 1614), 0.8 mM VPA (Sigma, dissolved in H2O) and 5 µM Y27632 (Millipore 688000). TOM = Advanced DMEM/F12, N2 supplement (at manufacturer’s recommended concentration), B27 supplement minus vitamin A (at manufacturer’s recommended concentration), Primocin 100 μg/mL, N-Acetyl-L-cysteine 1.25 mM, L-glutamine 2 mM, recombinant human EGF 50 ng/mL, CHIR99021 1.5 µM, recombinant human R-spondin-1 80 ng/mL, recombinant human FGF-2 100 ng/mL, recombinant human HGF 50 ng/mL, A83-01 500 nM, prostaglandin E2 2.5 µM, Y-27632 5 µM. EVT media 1 = Advanced DMEM/F12 (or DMEM/F12 for TSC-EVTM 2D), L-glutamine 2 mM, 2-mercaptoethanol 0.1 mM, penicillin/streptomycin solution 0.5% (vol/vol), BSA 0.3% (vol/vol, WAKO), ITS-X supplement 1% (vol/vol), NRG1 (Cell Signaling 5218SC) 100 ng/mL, A83-01 7.5 µM, Knockout serum replacement 4% (vol/vol) EVT media 2 = Advanced DMEM/F12 (or DMEM/F12 for TSC-EVTM 2D), L-glutamine 2 mM, 2-mercaptoethanol 0.1 mM, penicillin/streptomycin solution 0.5% (vol/vol), BSA 0.3% (vol/vol, WAKO), ITS-X supplement 1% (vol/vol), A83-01 7.5 µM, Knockout serum replacement 4% (vol/vol) ie: EVT medium cat. no. 1 without NRG1. Store the medium at 4°C for up to 1 week. EVT media 3 = DMEM/F12 (for TSC-EVTM 2D), L-glutamine 2 mM, 2-mercaptoethanol 0.1 mM, penicillin/streptomycin solution 0.5% (vol/vol), BSA 0.3% (vol/vol, WAKO), ITS-X supplement 1% (vol/vol), A83-01 7.5 µM, ie: EVT medium cat. no. 1 without NRG1 nor knockout serum replacement. Store the medium at 4°C for up to 1 week. Organoids were enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37 °C for 9 min. The disaggregated cell suspension was diluted with medium and passed through a 100-μm cell sieve (Corning, 431752). The disaggregated cell suspension was diluted with medium and passed through a 100-μm cell sieve (Corning, 431752). Cells obtained from both enzyme digests were pooled together and passed through a 100-μm cell sieve (Corning, 431752) and washed in Ham’s F12. The flow-through was centrifuged and resuspended in 5 ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10 min. Cells were loaded according to the manufacturer’s protocol for the Chromium Single Cell 3′ Kit v3.1 (10X Genomics). Library preparation was carried out according to the manufacturer’s protocol to attain between 2,000 and 10,000 cells per reaction.

text: normal

characteristic: disease

text: extravillous trophoblast medium

characteristic: growth condition

text: Primary Trophoblast Organoids

characteristic: in vitro system

text: Homo sapiens

text: Homo sapiens

text: embryo

characteristic: organism part

text: scRNA-seq

characteristic: protocol

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

text: public

text: ArrayExpress

text: trophoblast cell

text: human

characteristic: common name

text: normal

text: trophoblast organoid medium

text: Primary Trophoblast Organoids

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryo

text: scRNA-seq

text: Homo sapiens


characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: trophoblast cell

text: human

text: normal

text: trophoblast organoid medium

text: Primary Trophoblast Organoids

text: Homo sapiens

text: Homo sapiens

text: embryo

text: snRNA-seq

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:Wellcome Sanger Institute, Cambridge, UK

characteristic: Submitter Id

unit: week

characteristic: age

text: ArrayExpress

text: human

text: Protocols: Tissue samples used for this study were obtained with written informed consent from all participants in accordance with the guidelines in The Declaration of Helsinki 2000. Single-nuclei suspensions were isolated from frozen tissue sections when performing multiomic snRNA-seq/scATAC-seq. Thick (300 µm) sections were cryosectioned, and kept in a tube on dry ice until subsequent processing. Nuclei were released via Dounce homogenisation as described in detail in the protocols.io of PMID:26890679 For snRNA-seq/scATAC-seq experiments, cells were loaded according to the manufacturer’s protocol for the Chromium Single Cell Multiome ATAC + Gene Expression v1.0 to attain between 2,000 and 10,000 nucleus per well.

text: embryo

characteristic: developmental stage

text: normal

characteristic: individual

characteristic: multiome library pair

text: Homo sapiens

text: Homo sapiens

text: placenta

text: snucATAC-seq

text: maternal fetal interface

characteristic: sampling site

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: Wellcome Sanger Institute, Cambridge, UK

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: placenta

characteristic: organism part

text: snucATAC-seq

characteristic: protocol

text: maternal fetal interface

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

characteristic: common name

text: embryo

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: placenta

text: snucRNA-seq

text: maternal fetal interface

text: Homo sapiens

characteristic: title


characteristic: ENA-LAST-UPDATE

text: University of Copenhagen

characteristic: INSDC first public

text: public

characteristic: SRA accession

tag: Namespace:University of Copenhagen

characteristic: Submitter Id

text: gut metagenome

text: gut metagenome


characteristic: ENA-CHECKLIST

text: Umea University

text: public

characteristic: INSDC status

tag: Namespace:Umea University

text: Bacterial 16S rDNA (V4 region) obtained from stool

text: mouse gut metagenome

text: mouse gut metagenome

text: WT

characteristic: strain


text: Umea University

text: public

characteristic: description

text: mouse gut metagenome

text: mouse gut metagenome


text: DALHOUSIE UNIVERSITY

text: public

tag: Namespace:DALHOUSIE UNIVERSITY

text: human-gut

characteristic: broad-scale environmental context

text: not provided

characteristic: collection date

text: stool sample from pediatric oncology patient

text: feces

characteristic: environmental medium

text: Canada

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: local environmental context

text: human gut metagenome

text: MARITIME ONCOLOGY

characteristic: project name

text: human gut metagenome

text: MGS sequences from stool microbiome


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DALHOUSIE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: human-gut

text: not provided

text: stool sample from healthy relative of oncology patient

text: feces

text: Canada

text: human-gut

text: human gut metagenome

characteristic: organism

text: MARITIME ONCOLOGY

text: human gut metagenome

text: MGS sequences from stool microbiome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: DEPT OF MICROBIOLOGY

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae D6184/18-Greece

text: Greece

text: diseased

characteristic: host health state

text: homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Bronchial aspirate

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided

characteristic: serovar


text: DEPT OF MICROBIOLOGY

text: public

characteristic: collection date

text: Klebsiella pneumoniae C833/21-Greece

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: diseased

text: homo sapiens

text: Wound

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DEPT OF MICROBIOLOGY

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: Klebsiella pneumoniae A5051/21-Greece

text: Greece

text: diseased

text: homo sapiens

text: blood

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: DEPT OF MICROBIOLOGY

text: public

text: Klebsiella pneumoniae D2856/21-Greece

text: Greece

text: diseased

text: homo sapiens

text: Bronchial aspirate

text: not provided

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

text: not provided

characteristic: title


text: DEPT OF MICROBIOLOGY

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae C1909/21-Greece

text: Greece

text: diseased

text: homo sapiens

text: Wound

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


text: DEPT OF MICROBIOLOGY

text: public

text: Klebsiella pneumoniae A18940/21-Greece

text: Greece

text: diseased

characteristic: host health state

text: homo sapiens

characteristic: host scientific name

characteristic: isolate

text: blood

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided

characteristic: serovar


text: DEPT OF MICROBIOLOGY

text: public

characteristic: collection date

text: Klebsiella pneumoniae A7213/22-Greece

characteristic: description

text: Greece

characteristic: geographic location (country and/or sea)

text: diseased

text: homo sapiens

text: blood

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: DEPT OF MICROBIOLOGY

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: Klebsiella pneumoniae A9974/22-Greece

text: Greece

text: diseased

text: homo sapiens

text: blood

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: DEPT OF MICROBIOLOGY

text: public

text: Klebsiella pneumoniae A10037/22-Greece

text: Greece

text: diseased

text: homo sapiens

text: blood

text: not provided

text: Klebsiella pneumoniae

characteristic: organism

text: Klebsiella pneumoniae

text: not provided

characteristic: title


text: DEPT OF MICROBIOLOGY

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Klebsiella pneumoniae A10143/22-Greece

text: Greece

text: diseased

text: homo sapiens

text: blood

text: not provided

text: Klebsiella pneumoniae

text: Klebsiella pneumoniae

text: not provided


text: MAX PLANCK INSTITUTE BIOLOGY TUEBINGEN

text: public

tag: Namespace:MAX PLANCK INSTITUTE BIOLOGY TUEBINGEN

text: human metagenome

characteristic: common name

text: shotgun metagenome

text: human gut microbiome

characteristic: environment (biome)

text: gut

characteristic: environment (feature)

text: stool

characteristic: environment (material)

text: Colombia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: human-gut

characteristic: human gut environmental package

text: metagenome

characteristic: investigation type

text: human metagenome

text: Gut Metagenomes of Adult Colombians, Obesity and Cardiometabolic Health

characteristic: project name

text: human metagenome

text: HiSeq 3000

characteristic: sequencing method


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Tropical Medicine Antwerp

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ena-SAMPLE-TAB-09-02-2023-10:48:29:948-13590

tag: Namespace:Institute of Tropical Medicine Antwerp

text: Universidad Peruana Cayetano Heredia; Institute of Tropical Medicine Antwerp

characteristic: collecting institution

characteristic: collection date

text: Katlijn De Meulenaere, Elizabeth Villasis

characteristic: collector name

text: malaria parasite P. vivax

text: leukocyte-depleted blood sample from P. vivax patient from the Peruvian Amazon. Isolate was not cultured.

characteristic: description

text: 90% ring stages, 10% other blood stages

text: microscopy

characteristic: diagnostic method

text: Peru

characteristic: geographic location (country and/or sea)

text: Loreto, Zungarococha

characteristic: geographic location (region and locality)

text: human

characteristic: host common name

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: blood

characteristic: isolation source host-associated

text: Plasmodium vivax

text: Plasmodium vivax


name: E-MTAB-12628:Cappable-seq with constitutive MarA expression replicate 1

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF BIRMINGHAM

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:UNIVERSITY OF BIRMINGHAM

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: Protocols: S. Typhimurium strain SL1344 was grown to mid-log phase in LB medium. RNA was extracted using SV Total RNA Isolation System (Promega). Libraries were prepared as described by Warman et al. (2021) Nat. Microbiol.6:746-756.

text: pAMNMmarA

characteristic: genotype

text: mid exponential phase

characteristic: growth condition

text: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

characteristic: organism

text: constitutive MarA expression

characteristic: phenotype

characteristic: replicate

characteristic: title


name: E-MTAB-12628:Cappable-seq with constitutive MarA expression replicate 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UNIVERSITY OF BIRMINGHAM

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: ArrayExpress

characteristic: description

text: pAMNMmarA

text: mid exponential phase

text: constitutive MarA expression


name: E-MTAB-12628:Cappable-seq with constitutive RamA expression replicate 1

characteristic: ENA-CHECKLIST

text: UNIVERSITY OF BIRMINGHAM

characteristic: INSDC first public

text: public

text: ArrayExpress

text: pAMNFramA

text: mid exponential phase

text: constitutive RamA expression


name: E-MTAB-12628:Cappable-seq with constitutive RamA expression replicate 2

text: UNIVERSITY OF BIRMINGHAM

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: pAMNFramA

text: mid exponential phase

text: constitutive RamA expression


name: E-MTAB-12628:Cappable-seq with constitutive SoxS expression replicate 1

text: UNIVERSITY OF BIRMINGHAM

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: pAMNFsoxS

text: mid exponential phase

text: constitutive SoxS expression


name: E-MTAB-12628:Cappable-seq with constitutive SoxS expression replicate 2

text: UNIVERSITY OF BIRMINGHAM

text: public

text: ArrayExpress

text: pAMNFsoxS

characteristic: genotype

text: mid exponential phase

characteristic: growth condition

text: constitutive SoxS expression


LMG 18909

text: LM-UGent

text: public

text: LMG 18909

text: Komagataeibacter intermedius LMG 18909

text: Switzerland

characteristic: geographic location (country and/or sea)

text: LMG 18909

characteristic: isolate

text: commercially available tea fungus beverage (Kombucha)

text: Komagataeibacter intermedius

characteristic: organism

text: Komagataeibacter intermedius

text: LMG 18909

characteristic: strain

text: Komagataeibacter intermedius LMG 18909


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

tag: Namespace:University Medical Center Hamburg-Eppendorf

text: non-responder; timepoint 1

text: human gut metagenome

text: human gut metagenome

characteristic: title


characteristic: External Id

text: University Medical Center Hamburg-Eppendorf

characteristic: INSDC center name

characteristic: INSDC last update

text: public

text: non-responder; timepoint 1

text: human gut metagenome

text: human gut metagenome


characteristic: ENA-CHECKLIST

characteristic: INSDC first public

text: public

text: non-responder; timepoint 2

characteristic: description

text: human gut metagenome

text: human gut metagenome


text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: non-responder; timepoint 3

text: human gut metagenome

text: human gut metagenome


text: public

text: responder; timepoint 1

text: human gut metagenome

text: human gut metagenome


text: public

text: responder; timepoint 2

text: human gut metagenome

text: human gut metagenome


text: public

text: responder; timepoint 3

text: human gut metagenome

text: human gut metagenome


text: Ghent University

text: public

tag: Namespace:Ghent University

characteristic: age

text: ArrayExpress

characteristic: broker name

text: CLB-GA

text: neuroblast (sensu Vertebrata)

text: human

characteristic: common name

text: Protocols: 107 separated single cells that were cross-linked with 2% formaldehyde for 10 min at room temperature, cells were lysed. Cells were grown in RPMI1640 medium supplemented with 10% foetal bovine serum, 2mM L-Glutamine and 100 IU/ml penicillin/streptaviding at 37°C in a 5% CO2 humid atmosphere. Cross-linked DNA was digested was digested using 200U of NlaIII (NEB #R0125S) as primary restriction enzyme. This was followed by proximity ligation using 50U of T4 DNA ligase (Roche #10799009001) and ligated DNA circles were de-cross-links overnight using proteinase K and purified with NucleoMag P-Beads (Macherey-Nagel, Düren, Germany) to obtain an intermediate 3C template. To generate the 4C template, DNA was redigested using 50U DpnII (NEB #0543S) as secondary antibody followed again by proximity ligation. Digestion and ligation efficiency were evaluated via agarose gel electrophoresis. Adaptor-containing reading and non-reading primers, specific to the viewpoints of interest, were designed to amplify all captured, interacting DNA fragments (SOX11 viewpoint reading = CCACCAAAATTTTCATCATG and non-reading = TCTTCTATGCATCCGATTCT; without adapter sequence). 4C-sequencing fragments were amplified using the Expand Long Template PCR System (Roche, 11681834001) and using High Pure PCR Product Purification kit (Roche #11732676001) and QIAquick PCR Purification kit (Qiagen #28106).

text: neuroblastoma

characteristic: disease

text: wild type genotype

characteristic: genotype

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: wild type

characteristic: phenotype

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Ghent University

text: public

text: ArrayExpress

text: KELLY

text: neuroblast (sensu Vertebrata)

text: human

text: neuroblastoma

text: wild type genotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: wild type

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: Ghent University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: SHEP

text: neuroblast (sensu Vertebrata)

text: human

characteristic: description

text: neuroblastoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: wild type

text: Homo sapiens

text: female


text: Ghent University

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: SK-N-AS

text: neuroblast (sensu Vertebrata)

text: human

text: neuroblastoma

text: wild type genotype

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: wild type

text: Homo sapiens

text: female


E-MTAB-12620:Sample 1

text: WIS

text: public

text: E-MTAB-12620:Sample 1

unit: month

text: ArrayExpress

text: adipose macrophage

text: house mouse

characteristic: common name

text: Protocols: Femora and tibiae, irradiated and non irradiated were isolated from two months DNMT3AMut, bone marrow was flushed in to 2 tubes. We have adopted a protocol developed by Rosen et.al. The protocol combines a density gradient centrifugation method optimized for adipose tissue followed by nuclei “cleanup” step by sorting. Nuclei were sorted to low binding Eppendorf tubes and library was prepared by the 10X genomics V3 3’ kit. Libraries were prepared by the 10X genomics V3 3’ kit.

text: adult

characteristic: developmental stage

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: bone marrow

characteristic: organism part

text: Mus musculus

text: male

text: Sample 1


E-MTAB-12620:Sample 2

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WIS

text: public

text: E-MTAB-12620:Sample 2

text: ArrayExpress

text: adipose macrophage

text: house mouse

text: adult

text: Mus musculus

characteristic: organism

text: Mus musculus

text: bone marrow

text: Mus musculus

text: male

characteristic: sex

text: Sample 2


E-MTAB-12613:Sample 1

characteristic: ENA-CHECKLIST

text: WIS

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-12613:Sample 1

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

text: Protocols: Bone marrow cells were collected from the femora and tibia bones. BM was flushed with a 1cc (23G) into IMDM (Iscove's Modified Dulbecco's Medium). The cells were enriched by a c-kit CD117 and sorted by FACS. RNA extraction was performed using the 10x V3 Chromium technology. Libraries were prepared by the 10X genomics V3 3’ kit.

text: adult

text: Dnmt3A KI heterozygote

text: IR

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: male

text: Sample 1

characteristic: title


E-MTAB-12613:Sample 2

text: WIS

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12613:Sample 2

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

text: hematopoietic stem cell

text: house mouse

characteristic: description

text: adult

text: Dnmt3A KI heterozygote

text: NIR

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: male

text: Sample 2


E-MTAB-12614:Sample 1

text: WIS

text: public

text: E-MTAB-12614:Sample 1

text: ArrayExpress

characteristic: broker name

text: hematopoietic stem cell

text: house mouse

characteristic: common name

text: Protocols: Bone marrow cells were collected from the femora and tibia bones. BM was flushed with a 1cc (23G) into IMDM (Iscove's Modified Dulbecco's Medium). The cells were enriched by a c-kit CD117 and sorted by FACS. RNA extraction was performed according to manufacturer's protocol. Libraries were generated according to Keren-Shaul et al MARS-seq protocol.

text: adult

characteristic: developmental stage

text: wt/DNMT3A KI

characteristic: genotype

text: Sample 1

characteristic: individual

text: Mus musculus

text: Mus musculus

text: bone marrow

text: Mus musculus

text: male

text: Sample 1


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: 2017-11-25 (04:00)

text: milk sample from 4221

text: common

characteristic: diet

text: a

characteristic: dim

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

characteristic: longitude

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

text: milk microbiota from cows fed diets differing in starch-to-fiber ratios


characteristic: ENA-CHECKLIST

text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 2017-11-26 (04:00)

text: milk sample from 4221

text: common

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: 2018-01-03 (04:00)

text: milk sample from 4221

characteristic: description

text: a

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: External Id

text: UCSDMI

text: public

text: 2017-01-04 (04:00)

text: milk sample from 4221

text: a

characteristic: diet

text: a

characteristic: dim

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: 2017-03-14 (04:00)

text: milk sample from 4221

text: b

text: a

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-03-15 (04:00)

text: milk sample from 4221

text: b

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: longitude

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2017-11-25 (04:00)

text: milk sample from 4403

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

characteristic: other

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 2017-11-26 (04:00)

text: milk sample from 4403

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: 4403-D2 replicate, milk sample from 4403

characteristic: description

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: 4403-D2 replicate, milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: 2018-01-03 (04:00)

text: milk sample from 4403

text: b

characteristic: diet

text: b

characteristic: dim

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-01-04 (04:00)

text: milk sample from 4403

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

characteristic: longitude

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2017-03-14 (04:00)

text: milk sample from 4403

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

characteristic: other

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 2017-03-15 (04:00)

text: milk sample from 4403

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UCSDMI

text: public

text: 2017-11-25 (04:00)

text: milk sample from 4668

characteristic: description

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: milk sample from 4668

text: common

characteristic: diet

text: b

characteristic: dim

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: 4668-D2 replicate, milk sample from 4668

text: common

text: b

text: not collected

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

characteristic: longitude

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: 4668-D2 replicate, milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: 2018-01-03 (04:00)

text: milk sample from 4668

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 2017-01-04 (04:00)

text: milk sample from 4668

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: 2017-03-14 (04:00)

text: milk sample from 4668

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


characteristic: External Id

text: UCSDMI

text: public

text: 2017-03-15 (04:00)

text: milk sample from 4668

characteristic: description

text: a

characteristic: diet

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: 2017-11-25 (04:00)

text: milk sample from 4889

text: common

text: b

characteristic: dim

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: milk sample from 4889

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

characteristic: longitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2018-01-03 (04:00)

text: milk sample from 4889

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: 2017-01-04 (04:00)

text: milk sample from 4889

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

characteristic: Submitter Id

text: 2017-03-14 (04:00)

text: milk sample from 4889

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: External Id

text: UCSDMI

text: public

text: 2017-03-15 (04:00)

text: milk sample from 4889

characteristic: description

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


text: UCSDMI

text: public

text: 2017-11-25 (04:00)

text: milk sample from 5002

text: common

characteristic: diet

text: b

characteristic: dim

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: milk sample from 5002

text: common

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2018-01-03 (04:00)

text: milk sample from 5002

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: longitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 2017-01-04 (04:00)

text: milk sample from 5002

text: b

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

characteristic: SRA accession

text: 2017-03-14 (04:00)

text: milk sample from 5002

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: External Id

text: UCSDMI

text: public

characteristic: Submitter Id

text: 2017-03-15 (04:00)

text: milk sample from 5002

characteristic: description

text: a

text: b

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: 2017-11-25 (04:00)

text: milk sample from 5007

text: common

characteristic: diet

text: a

characteristic: dim

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: 2017-11-26 (04:00)

text: milk sample from 5007

text: common

text: a

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: 2018-01-03 (04:00)

text: milk sample from 5007

text: a

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: 2017-01-04 (04:00)

text: milk sample from 5007

text: a

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: longitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: UCSDMI

text: public

text: 2017-03-14 (04:00)

text: milk sample from 5007

text: b

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

characteristic: organism

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: External Id

text: UCSDMI

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: 2017-03-15 (04:00)

text: milk sample from 5007

text: b

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


text: UCSDMI

text: public

text: yes

text: 2017-11-25 (04:00)

text: milk sample from 5020

characteristic: description

text: common

characteristic: diet

text: a

characteristic: dim

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: hoof.infection.treated.nov18-nov21.polyflex.nov.18.flunixin

characteristic: other

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no


characteristic: ENA-CHECKLIST

text: UCSDMI

text: public

text: yes

text: 2017-11-26 (04:00)

text: milk sample from 5020

text: common

text: a

characteristic: elevation

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

characteristic: host scientific name

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no

characteristic: title


text: UCSDMI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: yes

text: 2018-01-03 (04:00)

text: milk sample from 5020

text: a

text: a

text: Host-associated

text: Host-associated (non-saline)

text: Animal (non-saline)

text: Animal secretion (non-saline)

text: rangeland biome

text: agricultural feature

text: milk

text: host-associated

text: Bos taurus

text: not collected

text: not collected

text: UBERON:milk

text: UBERON:milk

text: UBERON:milk

text: cow

text: not collected

text: not collected

text: not collected

text: not collected

characteristic: latitude

text: bovine metagenome

text: Western Human Nutrition Research Center

text: milk

text: milk

text: bovine metagenome

text: no