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characteristic: INSDC status

tag: Namespace:Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden

text: ArrayExpress

characteristic: broker name

text: kidney cell

text: not collected

text: human

characteristic: common name

text: Protocols: CUT&RUN for CTCF was performed as described in (PMID: 29651053), with minor modifications as described here. Three independent rounds of experiments were performed for the three biological replicates of each cell line and condition. 250,000 cells were used per replicate. Antibodies used included anti-CTCF (abcam, ab70303) and anti-HA (Merck, 05-902R) at 1:100 dilutions. For each replicate of CTCF, a corresponding anti-HA negative control was performed from cells in the same well. 40 µl of ConA beads were used per sample, and digitonin concentration was 0.025% throughout the protocol. CUT&RUN LoV-U for H3K4me3, H3K4me1 and H3K27ac was performed according to (PMID: 36355069), based originally on (PMID: 29651053), with minor modifications as described here. Experiments were performed in duplicate for each condition. 250,000 cells were used per sample and bound to 10 µl magnetic ConA agarose beads. Antibodies used included anti-H3K4me3 (antibodies online, ABIN6971977), anti-H3K4me1 (antibodies online, ABIN3023251), and anti-H3K27ac (antibodies online, ABIN2668475) at 1:100 dilutions. The digestion buffer was kept and added to the release fraction before DNA purification. HEK293T human embryonic kidney cells (parental) and Δβ-catenin cells (generated in PMID: 30425074) were cultured in a 37 °C incubator in 5% CO2 and 89% humidity. Culture medium used was high glucose Dulbecco’s Modified Eagle Medium (Cat. #41965039, Gibco) supplemented with 10 % bovine calf serum (Cat. #1233C, Sigma-Aldrich) and 1X Penicillin-Streptomycin (Cat. #15140148, Gibco). Cells were stimulated either with 10 µM CHIR99021 (Wnt ON) or 1 nM LGK (Wnt OFF) for 24 hr prior to harvest for assays. DNA was purified with phenol:chloroform:isoamyl alcohol followed by ethanol precipitation, and stored until library preparation. Library preparation was performed according to PMID: 36355069 using the KAPA Hyperprep Kit (KAPA Biosystems, Cat. #KK8504) with the following modifications: for CTCF samples, 15 cycles of amplification were performed, while LoV-U samples received 13 cycles as previously described. For CTCF samples, size selection was performed post-amplification using 2% E-Gel Size Select II Gels (Thermo Fisher, Cat #G661012), retrieving fragments from 150 – 240 bp (representing 30 – 120 bp without the adapter sequences).

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

text: ArrayExpress

text: kidney cell

text: not collected

text: human

text: embryo stage

text: normal

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: kidney cell

text: not collected

characteristic: collection date

text: human

text: Protocols: Flasks were taken from the incubator and fresh methanol-free formaldehyde 16% was added to the culture media to a final concentration of 1%. Fixation proceed at RT for 15 minutes, and was then quenched with cold glycine to 150 mM and incubated for 5 min RT. Media was removed and cells were washed twice with cold PBS. Cells were harvested in PBS using a scraper, transferred to a chilled tube, and pelleted at 4 dgrees for 5 minutes. Supernatant was discarded and the cell pellet was flash frozen and store at -80 degrees until HiChIP. HEK293T human embryonic kidney cells (parental) and Δβ-catenin cells (generated in PMID: 30425074) were cultured in a 37 °C incubator in 5% CO2 and 89% humidity. Culture medium used was high glucose Dulbecco’s Modified Eagle Medium (Cat. #41965039, Gibco) supplemented with 10 % bovine calf serum (Cat. #1233C, Sigma-Aldrich) and 1X Penicillin-Streptomycin (Cat. #15140148, Gibco). Cells were stimulated either with 10 µM CHIR99021 (Wnt ON) or 1 nM LGK (Wnt OFF) for 24 hr prior to harvest for assays. HiChIP was performed in duplicates in both LGK (Wnt-off) and CHIR99021 (Wnt ON) cell lines using the Arima-HiC+ Kit (A101020) and according to the guidelines in the Arima-HiChIP user guide for mammalian cells. HEK293T cells were cultured as described above and stimulated for 24 hours for Wnt ON and Wnt OFF, and approximately 5 × 106 cells per line were used to obtain at least 15 μg of input DNA for HiChIP. Cells were fixed in 1% fresh methanol-free formaldehyde for 15 min at room temperature while rotating, and Glycine was used to quench the crosslinking reaction (final concentration 125 mM Glycine) for 5 min. After two washes with cold PBS, crosslinked cells were harvested in PBS by scraping, pelleted and stored at -80°C until further used. In the subsequent steps, crosslinked chromatin was digested with restriction enzymes, end-filled with biotinylated nucleotides and ligated. Proximally ligated chromatin was then sheared on a Covaris E22O instrument, with the following shearing parameters: shearing time 5 min, PIP 105, duty factor 5, and 200 cycles per burst), to achieve a fragment size range of 200 bp to 800 bp. Chromatin immunoprecipitation was performed with an antibody against CTCF (AbFlex CTCF , Active Motif, Catalog Nos:91285, Lot No:31321002), using 0.5 g of antibody per g of sheared chromatin. After biotin enrichment and adapters ligation, immunoprecipitated DNA was subjected to PCR amplification (18 cycles) using Accel-NGS 2 S Plus DNA Library Kit (#21024, Swift Biosciences) and indexing Kit (#26696, Swift Biosciences), according to the Arima-HiChIP Library Prep user guide.

text: embryo stage

text: normal

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: public

text: ArrayExpress

characteristic: broker name

text: kidney cell

text: not collected

text: human

characteristic: common name

text: Protocols: RUW regions were amplified from genomic DNA of transfected populations via PCR with the high fidelity Q5 polymerase (New England Biolabs, Cat. # M0491S), with an annealing temperature of 62 degrees and performing 35 cycles. HEK293T human embryonic kidney cells (parental) and Δβ-catenin cells (generated in PMID: 30425074) were cultured in a 37 °C incubator in 5% CO2 and 89% humidity. Culture medium used was high glucose Dulbecco’s Modified Eagle Medium (Cat. #41965039, Gibco) supplemented with 10 % bovine calf serum (Cat. #1233C, Sigma-Aldrich) and 1X Penicillin-Streptomycin (Cat. #15140148, Gibco). Cells were stimulated either with 10 µM CHIR99021 (Wnt ON) or 1 nM LGK (Wnt OFF) for 24 hr prior to harvest for assays. Correct product size and a single product was confirmed with an agarose gel, then the DNA was purified with bead cleanup to remove primers and contaminants. Library preparation was performed according to PMID: 36355069 using the KAPA Hyperprep Kit (KAPA Biosystems, Cat. #KK8504) with the following modifications: for CTCF samples, 15 cycles of amplification were performed, while LoV-U samples received 13 cycles as previously described. For CTCF samples, size selection was performed post-amplification using 2% E-Gel Size Select II Gels (Thermo Fisher, Cat #G661012), retrieving fragments from 150 – 240 bp (representing 30 – 120 bp without the adapter sequences).

characteristic: description

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: genotype

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Centre for Microbiology and Environmental Systems Science

text: Catovirus naegleriensis strain 1, a giant virus infecting Naegleria spp. genome sequencing from isolated viral particles

text: Austria

characteristic: geographic location (country and/or sea)

text: Klosterneuburg

characteristic: geographic location (region and locality)

text: Naegleria clarki

text: Catovirus sp. 'naegleriensis'

text: Catovirus sp. 'naegleriensis'

characteristic: strain


text: HUN-REN

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: 5 different lineages of ciprofloxacin treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

characteristic: organism

text: Mycolicibacterium smegmatis MC2 155

text: Ciprofloxacin treated Mycobacterium smegmatis


text: HUN-REN

text: public

characteristic: collection date

text: 6 different lineages of rifampicin treated Mycobacterium smegmatis, 60 days treatment

characteristic: description

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Rifampicin treated Mycobacterium smegmatis

characteristic: title


characteristic: ENA-CHECKLIST

text: HUN-REN

text: public

text: 5 different lineages of rifampicin treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155


characteristic: ENA-FIRST-PUBLIC

text: HUN-REN

text: public

text: 5 different lineages of isoniazid treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Isoniazid treated Mycobacterium smegmatis


characteristic: ENA-LAST-UPDATE

text: HUN-REN

text: public

text: 5 different lineages of ethambutol treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Ethambutol treated Mycobacterium smegmatis


characteristic: External Id

text: HUN-REN

text: public

text: 6 different lineages of ethambutol treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155


text: HUN-REN

text: public

text: 5 different lineages of pyrazinamide, ethamubtol, isoniazid and rifampicin treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

characteristic: geographic location (country and/or sea)

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Combination of first line TB drugs treated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 6 different lineages of pyrazinamide, ethamubtol, isoniazid and rifampicin treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155


text: HUN-REN

text: public

text: 5 different lineages of mitomycinC treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: MitomycinC treated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 5 different lineages of UV radiation treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: UV treated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 6 different lineages of UV radiation treated Mycobacterium smegmatis, 60 days treatment

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: UV treated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 5 different lineages of untreated Mycobacterium smegmatis, 120 days

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Untreated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 5 different lineages of untreated Mycobacterium smegmatis, 60 days

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Untreated Mycobacterium smegmatis


text: HUN-REN

text: public

text: 6 different lineages of untreated Mycobacterium smegmatis, 60 days

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Untreated Mycobacterium smegmatis


APAW

text: HUN-REN

text: public

text: APAW

text: Common ancestor of every treated and untreated lineages, wild-type Mycobacterium smegmatis, untreated

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Untreated Mycobacterium smegmatis


text: HUN-REN

text: public

text: Wild-type Mycobacterium smegmatis, untreated

text: Hungary

text: Mycolicibacterium smegmatis MC2 155

text: Mycolicibacterium smegmatis MC2 155

text: Untreated Mycobacterium smegmatis


text: NTNU

text: public

text: HaCaT/MEF

text: not collected

text: human

characteristic: common name

text: Human keratinocyte (HaCaT) and mouse embryonic fibroblast (MEF) cells mixed 9 to 1

text: Norway

text: Homo sapiens

text: Homo sapiens

text: HaCaT and MEF mixed sample, replicate A


text: NTNU

text: public

text: HaCaT/MEF

text: not collected

text: human

text: Norway

text: Homo sapiens

text: Homo sapiens

text: HaCaT and MEF mixed sample, replicate B


text: public

tag: Namespace:Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Respiratory Virus Unit, Microbiology Services Colindale, Public Health England

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: title

text: not provided


characteristic: ENA first public

text: public

text: public

characteristic: Secondary Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

text: NCBI

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: receipt date

characteristic: sample capture status

characteristic: sample name

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

text: not provided

characteristic: serotype (required for a seropositive sample)

characteristic: title

text: not provided

characteristic: virus identifier


text: West of Scotland Specialist Virology Centre, NHSGGC / MRC-University of Glasgow Centre for Virus Research

text: public

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

text: Scotland

characteristic: geographic location (region and locality)

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: sample capture status

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Tree of Life Programme

characteristic: Submitter Id

text: Amjad Khalaf

text: Wellcome Sanger Institute

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Wellcome Genome Campus

text: Terrestrial

characteristic: habitat

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

characteristic: lifestage

text: Oecophylla smaragdina

text: WHOLE ORGANISM

characteristic: organism part

text: ToL

characteristic: project name

text: Oecophylla smaragdina

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

text: public

text: Kamil Jaron

text: University of Edinburgh

characteristic: collecting institution

text: United Kingdom

text: Wytham Woods

characteristic: geographic location (region and locality)

text: Terrestrial

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

text: Oecophylla smaragdina

characteristic: organism

text: WHOLE ORGANISM

text: ToL

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N

characteristic: title


text: Sanger Institute

text: FD17259889 DNA

text: Tree of Life Programme

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Amjad Khalaf

text: Wellcome Sanger Institute

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Wellcome Genome Campus

text: Terrestrial

characteristic: habitat

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

text: Oecophylla smaragdina

text: ABDOMEN

characteristic: sample derived from

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: FD17259889 HIC

text: Tree of Life Programme

text: public

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: United Kingdom

text: Wellcome Genome Campus

text: Terrestrial

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

characteristic: lifestage

text: Oecophylla smaragdina

text: THORAX

characteristic: organism part

characteristic: project name

text: Oecophylla smaragdina

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: N

characteristic: symbiont

characteristic: tolid


text: Sanger Institute

text: FD17259945 DNA

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Amjad Khalaf

text: Wellcome Sanger Institute

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

text: Wellcome Genome Campus

characteristic: geographic location (region and locality)

text: Terrestrial

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

text: Oecophylla smaragdina

characteristic: organism

text: ABDOMEN

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: FD17259945 HIC

text: Tree of Life Programme

text: public

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: United Kingdom

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Wellcome Genome Campus

text: Terrestrial

characteristic: habitat

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

characteristic: lifestage

text: Oecophylla smaragdina

text: THORAX

characteristic: sample derived from

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N


text: Sanger Institute

text: FD22333472 DNA

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Kamil Jaron

text: University of Edinburgh

text: United Kingdom

text: Wytham Woods

text: Terrestrial

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

text: Oecophylla smaragdina

text: ABDOMEN

characteristic: organism part

characteristic: project name

text: Oecophylla smaragdina

text: NOT COLLECTED

characteristic: sex

text: NOT APPLICABLE

text: N

characteristic: symbiont

characteristic: tolid


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Sanger Institute

characteristic: GAL

text: FD22333604 DNA

text: Tree of Life Programme

text: public

text: Amjad Khalaf

text: Wellcome Sanger Institute

characteristic: collecting institution

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Wellcome Genome Campus

characteristic: geographic location (region and locality)

text: Terrestrial

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

text: Oecophylla smaragdina

characteristic: organism

text: ABDOMEN

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N

characteristic: title


text: Sanger Institute

text: FD22333604 HIC

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: United Kingdom

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Wellcome Genome Campus

text: Terrestrial

characteristic: habitat

text: Amjad Khalaf

text: Wellcome Sanger Institute

text: adult

characteristic: lifestage

text: Oecophylla smaragdina

text: THORAX

characteristic: sample derived from

text: Oecophylla smaragdina

text: NOT COLLECTED

text: NOT APPLICABLE

text: N


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

tag: Namespace:Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

text: SIB

characteristic: broker name

text: Hôpital Cantonal de Fribourg - HFR, CH-1752 Villars-sur-Glâne, Switzerland

characteristic: collecting institution

text: Trestan Pillonel, Damien Jacot, Sébastien Aeby, Gilbert Greub, Claire Bertelli

characteristic: collector name

text: Switzerland

text: VD

text: Human

characteristic: host common name

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/VD-CHUV-GEN19011/2023

characteristic: isolate

text: active surveillance not initiated by an outbreak

characteristic: sample capture status


text: Laboratory of genomics and metagenomics, Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: CHUV, CH-1011 Lausanne, Switzerland

characteristic: collection date

text: Switzerland

characteristic: geographic location (country and/or sea)

text: VD

characteristic: geographic location (region and locality)

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/VD-CHUV-GEN18963/2023

characteristic: organism

characteristic: title


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text: ETH ZURICH

text: public

text: blood

text: cattle

text: male

text: Switzerland

text: Bos taurus

text: Bos taurus

text: RGVxSIM


text: public

characteristic: broker name

characteristic: collecting institution

text: unknown

characteristic: collector name

text: Slovakia

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: unknown

characteristic: host subject id

text: RNA

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UTRECHT UNIVERSITY

text: public

characteristic: SRA accession

tag: Namespace:UTRECHT UNIVERSITY

characteristic: Submitter Id

characteristic: collection date

text: Cellulophaga lytica HM-01

text: Netherlands

characteristic: geographic location (country and/or sea)

text: Cellulophaga lytica

characteristic: organism

text: Cellulophaga lytica

text: Cellulophaga lytica HM-01


text: UTRECHT UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Algibacter lectus HM-02

characteristic: description

text: Netherlands

text: Algibacter lectus

text: Algibacter lectus

text: Algibacter lectus HM-02

characteristic: title


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-03

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-03


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-04

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-04


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-05

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-05


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter adhaerens HM-06

text: Netherlands

text: Marinobacter adhaerens

text: Marinobacter adhaerens

text: Marinobacter adhaerens HM-06


text: UTRECHT UNIVERSITY

text: public

text: Flexithrix dorotheae HM-07

text: Netherlands

text: Flexithrix dorotheae

text: Flexithrix dorotheae

text: Flexithrix dorotheae HM-07


text: UTRECHT UNIVERSITY

text: public

text: Maribacter dokdonensis HM-08

text: Netherlands

text: Maribacter dokdonensis

text: Maribacter dokdonensis

text: Maribacter dokdonensis HM-08


text: UTRECHT UNIVERSITY

text: public

text: Gillisia mitskevichiae HM-09

text: Netherlands

text: Gillisia mitskevichiae

text: Gillisia mitskevichiae

text: Gillisia mitskevichiae HM-09


text: UTRECHT UNIVERSITY

text: public

text: Flavobacterium antarcticum HM-10

text: Netherlands

text: Flavobacterium antarcticum

text: Flavobacterium antarcticum

text: Flavobacterium antarcticum HM-10


text: UTRECHT UNIVERSITY

text: public

text: Cyclobacterium marinum HM-11

text: Netherlands

text: Cyclobacterium marinum

text: Cyclobacterium marinum

text: Cyclobacterium marinum HM-11


text: UTRECHT UNIVERSITY

text: public

text: Zunongwangia profunda HM-12

text: Netherlands

text: Zunongwangia profunda

text: Zunongwangia profunda

text: Zunongwangia profunda HM-12


text: UTRECHT UNIVERSITY

text: public

text: Gramella echinicola HM-13

text: Netherlands

text: Christiangramia echinicola

text: Christiangramia echinicola

text: Gramella echinicola HM-13


text: UTRECHT UNIVERSITY

text: public

text: Gramella forsetii HM-14

text: Netherlands

text: Christiangramia forsetii

text: Christiangramia forsetii

text: Gramella forsetii HM-14


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga pacifica HM-15

text: Netherlands

text: Cellulophaga pacifica

text: Cellulophaga pacifica

text: Cellulophaga pacifica HM-15


text: UTRECHT UNIVERSITY

text: public

text: Zooshikella ganghwensis HM-19

text: Netherlands

text: Zooshikella ganghwensis

text: Zooshikella ganghwensis

text: Zooshikella ganghwensis HM-19


text: UTRECHT UNIVERSITY

text: public

text: Enterobacter asburiae HM-20

text: Netherlands

text: Enterobacter asburiae

text: Enterobacter asburiae

text: Enterobacter asburiae HM-20


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-21

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-21


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-22

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-22


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-23

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-23


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-24

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-24


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-25

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-25


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-26

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-26


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-27

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-27


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-28

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-28


text: UTRECHT UNIVERSITY

text: public

text: Muricauda flavescens HM-29

text: Netherlands

text: Allomuricauda flavescens

text: Allomuricauda flavescens

text: Muricauda flavescens HM-29


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-30

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-30


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter pelagius HM-31

text: Netherlands

text: Marinobacter pelagius

text: Marinobacter pelagius

text: Marinobacter pelagius HM-31


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-32

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-32


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-33

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-33


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-34

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-34


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-35

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-35


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-36

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-36


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-37

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-37


text: UTRECHT UNIVERSITY

text: public

text: Virgibacillus dokdonensis HM-38

text: Netherlands

text: Virgibacillus dokdonensis

text: Virgibacillus dokdonensis

text: Virgibacillus dokdonensis HM-38


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-39

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-39


text: UTRECHT UNIVERSITY

text: public

text: Muricauda ruestringensis HM-40

text: Netherlands

text: Allomuricauda ruestringensis

text: Allomuricauda ruestringensis

text: Muricauda ruestringensis HM-40


text: UTRECHT UNIVERSITY

text: public

text: Algicola bacteriolytica HM-41

text: Netherlands

text: Algicola bacteriolytica

text: Algicola bacteriolytica

text: Algicola bacteriolytica HM-41


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter adhaerens HM-42

text: Netherlands

text: Marinobacter adhaerens

text: Marinobacter adhaerens

text: Marinobacter adhaerens HM-42


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-43

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-43


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter adhaerens HM-44

text: Netherlands

text: Marinobacter adhaerens

text: Marinobacter adhaerens

text: Marinobacter adhaerens HM-44


text: UTRECHT UNIVERSITY

text: public

text: Tenacibaculum gallaicum HM-45

text: Netherlands

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum HM-45


text: UTRECHT UNIVERSITY

text: public

text: Tenacibaculum gallaicum HM-46

text: Netherlands

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum HM-46


text: UTRECHT UNIVERSITY

text: public

text: Tenacibaculum gallaicum HM-47

text: Netherlands

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum

text: Tenacibaculum gallaicum HM-47


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga pacifica HM-48

text: Netherlands

text: Cellulophaga pacifica

text: Cellulophaga pacifica

text: Cellulophaga pacifica HM-48


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-49

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-49


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-50

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-50


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-51

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-51


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-52

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-52


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-53

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-53


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-54

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-54


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-55

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-55


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-56

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-56


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-57

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-57


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-58

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-58


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-59

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-59


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-60

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-60


text: UTRECHT UNIVERSITY

text: public

text: Maribacter forsetii HM-61

text: Netherlands

text: Maribacter forsetii

text: Maribacter forsetii

text: Maribacter forsetii HM-61


text: UTRECHT UNIVERSITY

text: public

text: Maribacter dokdonensis HM-62

text: Netherlands

text: Maribacter dokdonensis

text: Maribacter dokdonensis

text: Maribacter dokdonensis HM-62


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga lytica HM-63

text: Netherlands

text: Cellulophaga lytica

text: Cellulophaga lytica

text: Cellulophaga lytica HM-63


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter algicola HM-64

text: Netherlands

text: Marinobacter algicola

text: Marinobacter algicola

text: Marinobacter algicola HM-64


text: UTRECHT UNIVERSITY

text: public

text: Alteromonas halophila HM-65

text: Netherlands

text: Alteromonas halophila

text: Alteromonas halophila

text: Alteromonas halophila HM-65


text: UTRECHT UNIVERSITY

text: public

text: Zooshikella ganghwensis HM-66

text: Netherlands

text: Zooshikella ganghwensis

text: Zooshikella ganghwensis

text: Zooshikella ganghwensis HM-66


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter sediminum HM-67

text: Netherlands

text: Marinobacter sediminum

text: Marinobacter sediminum

text: Marinobacter sediminum HM-67


text: UTRECHT UNIVERSITY

text: public

text: Kriegella aquimaris HM-68

text: Netherlands

text: Kriegella aquimaris

text: Kriegella aquimaris

text: Kriegella aquimaris HM-68


text: UTRECHT UNIVERSITY

text: public

text: Marinobacter sediminum HM-69

text: Netherlands

text: Marinobacter sediminum

text: Marinobacter sediminum

text: Marinobacter sediminum HM-69


text: UTRECHT UNIVERSITY

text: public

text: Algibacter lectus HM-73

text: Netherlands

text: Algibacter lectus

text: Algibacter lectus

text: Algibacter lectus HM-73


text: UTRECHT UNIVERSITY

text: public

text: Cellulophaga fucicola HM-74

text: Netherlands

text: Cellulophaga fucicola

text: Cellulophaga fucicola

text: Cellulophaga fucicola HM-74


text: UTRECHT UNIVERSITY

text: public

text: Algibacter lectus HM-75

text: Netherlands

text: Algibacter lectus

text: Algibacter lectus

text: Algibacter lectus HM-75


text: public

characteristic: broker name

characteristic: collecting institution

text: unknown

characteristic: collector name

text: Slovakia

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: unknown

characteristic: host subject id

text: RNA


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: unknown

text: Slovakia

text: Human

text: not provided

text: Homo sapiens

text: female

text: unknown

text: RNA

characteristic: isolate


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:CIIMAR - Interdisciplinary Centre of Marine and Environmental Research

text: marine biome

characteristic: broad-scale environmental context

unit: year-month-day

unit: m

characteristic: depth

text: Amplicon sequencing of the V4-V5 16S rRNA gene from seawater collected in the station KpN2 of Kongsfjorden, at 10m depth

characteristic: description

text: sea water

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: oceanic epipelagic zone biome

characteristic: local environmental context

text: marine metagenome

characteristic: organism

characteristic: project name

text: marine metagenome

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: CIIMAR - Interdisciplinary Centre of Marine and Environmental Research

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: marine biome

characteristic: collection date

text: Amplicon sequencing of the V4-V5 16S rRNA gene from seawater collected in the station CpS5 of Kongsfjorden, at 10m depth

text: sea water

text: Arctic Ocean

text: oceanic epipelagic zone biome

text: marine metagenome

text: marine metagenome


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: marine biome

characteristic: broad-scale environmental context

characteristic: depth

text: Amplicon sequencing of the V4-V5 16S rRNA gene from seawater collected in the station KB6 of Kongsfjorden, at 50m depth

text: sea water

text: Arctic Ocean

text: oceanic epipelagic zone biome

text: marine metagenome

text: marine metagenome


text: public

text: marine biome

text: Amplicon sequencing of the V4-V5 16S rRNA gene from seawater collected in the station KB6 of Kongsfjorden, at 5m depth

characteristic: description

text: sea water

characteristic: environmental medium

text: Arctic Ocean

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: oceanic epipelagic zone biome

characteristic: local environmental context

text: marine metagenome

text: marine metagenome