E-MTAB-12238:Sample 88

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

text: E-MTAB-12238:Sample 88

text: Repli G

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: date

text: adult

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria - H4100 colony

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 88

characteristic: title


E-MTAB-12238:Sample 89

status: PUBLIC

tag: attribute

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 89

tag: Namespace:Department of Molecular Cell Biology, Weizmann Institute of Science

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice. xenograft protocol: NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) mice (The Jackson Laboratory, Bar Harbor, Maine, USA) were maintained and bred under specific pathogen-free conditions at the Biomedical Core Facility (Faculty of Medicine, the Technion, Haifa, Israel). Twenty-four hours prior to transplantation, 8-12-week-old female NSG mice were sub-lethally irradiated with 225 cGy. Primary human cells were intra-femorally injected. The total number of cells transplanted per mouse depended on the number of viable cells obtained from the BM/PB of a patient [ranged from 1 colony (a single cell-derived subclone) to 106 cells]. The animals were sacrificed 8-30 weeks after transplantation or if tumors developed in the injected knee. The BM was then harvested. Human engraftment was evaluated by flow cytometry using the following anti-human specific antibodies: anti-CD45-APC Cyanine7 (APC-Cy7) (BioLegend #304014 clone H130); anti-CD33-BV510 (BioLegend #366610); anti-CD34-BV421 (BioLegend #343610); anti-CD38-FITC (BD #555459); anti-CD15 APC (BD #551376); anti-CD19 PE-CY7 (BD #557835); Cell viability was obtained using Propidium Iodide - PI (BioLegend #421301). Analyses were performed using FlowJo software v.10 (Treestar, OR, USA), and the expression of markers was assessed and presented as the percentage of stained cells. The threshold for engraftment detection was 0.1% of human CD45+ cells. All flow cytometry analyses were done using an LSR II (BD Bioscience, CA, USA) or FACSariaII (BD Bioscience, CA, USA) device. Engraftment of >5% of hCD45+ cells with the major CD33+ population (>60% of the hCD45+ cells) was classified as overt leukemia; the presence of 0.1-5% of hCD45+ cells or the presence of >5% of hCD45+ cells with <60% of the CD33+ population in the hCD45+ cells was classified as non-overt leukemia; and the presence of <0.1% of human CD45+ (hCD45+) population was considered as non-engraftment. hCD45+ cells were sorted and underwent whole genome amplification (WGA) for further genotyping assays. CD34+ cells were isolated from PB or BM (following mononuclear cell separation) of AML patients by positive selection using anti-human CD34 microbeads. Enriched CD34+ cells were sorted by FACSariaII (BD bioscience, CA, USA) into four subpopulations of HSPCs according to their surface markers and CD33 expression. The sorted fractions were collected either into Iscove's modified Dulbecco's medium (IMDM) +20% fetal bovine serum (FBS) (Biological Industries #02-023-1A) to be further used in the colony forming unit (CFU) assay or into PBS+2%FBS to be used in the xenotransplantation assay. The CFU assay was adjusted to the generation of single cell-derived subclones. HSPCs were seeded in 1% standard methylcellulose medium supplemented with 37% FBS, 1.2% bovine serum albumin (BSA), 1% L-glutamine, 10-6M b-mercaptoethanol, 1 IU/ml of human erythropoietin (EPO), 50 ng/ml of human stem cell factor (SCF), 25 ng/ml of human FLT3 ligand, 10 ng/ml of interleukin 3 (IL-3), 10 ng/ml of interleukin 6 (IL-6), 10 ng/ml of granulocytecolony stimulating factor (G-CSF), 5 ng/ml of granulocyte-macrophage colony-stimulating factor (GM-CSF), 10 ng/ml of human thrombopoietin (TPO), 100 IU ml penicillin and 100 mg/ml streptomycin. Colonies were counted after 14 days and each of them was picked under sterile conditions. Every individual colony was divided into two cell suspensions to perform both genotyping analysis and xenotransplantation into NSG mice One µl of DNA template was added to a hybridization mix together with an MIP pool (final concentration of 0.05pM per probe) in 1x Ampligase buffer (Epicentre). The mix was incubated in a thermal cycler according to the following program: 98°C for 3 minutes, 85°C for 30 minutes, 60°C for 60 minutes and 56°C for 1 or 2 overnight incubations. The product was mixed with (final concentration in brackets): dNTPs (Larova, 15pM), Betaine (375 mM, Sigma-Aldrich,), NAD+ (1 mM, New England Biolabs), additional Ampligase buffer (0.5x), Ampligase (total of 1.25U, Epicentre) and Phusion HF (0.16U, New England Biolabs). The mix was incubated at 56°C for 60 minutes followed by 72°C for 20 minutes. Enzymatic digestion of linear probes was performed by adding Exonuclease I (4U, New England Biolabs) and Exonuclease III (25U, New England Biolabs). The mix was incubated at 37°C for 2 hours, followed by 80°C for 20 minutes. The final product was amplified using iProof HF Master Mix (Biorad). Samples were pooled and concentrated using AMPure XP beads (Beckman Coulter) at 1.3x volumetric concentration, size-selected (190-370bp) using Blue Pippin (Sage scientific), and sequenced in either NextSeq or Novaseq6000 (Illumina) 2X151bp paired-end run using custom primers as described in the past(Biezuner et al., 2022)

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-; CD45 positive

characteristic: subclone

characteristic: time

text: Sample 89

text: human CD45 positive out of mouse bone marrow 73

characteristic: xenograft


E-MTAB-12238:Sample 9

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Department of Molecular Cell Biology, Weizmann Institute of Science

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12238:Sample 9

text: Repli G

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: date

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: Sample 9

text: human CD45 positive out of mouse bone marrow 80


E-MTAB-12238:Sample 90

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 90

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: Sample 90

characteristic: title


E-MTAB-12238:Sample 91

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

text: E-MTAB-12238:Sample 91

text: Repli G

text: ArrayExpress

text: B cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

characteristic: date

text: adult

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: bone marrow

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

characteristic: time

text: Sample 91


E-MTAB-12238:Sample 92

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 92

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: B cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 92


E-MTAB-12238:Sample 93

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

text: E-MTAB-12238:Sample 93

text: Repli G

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: Sample 93

characteristic: title

text: human CD45 positive out of mouse bone marrow 89

characteristic: xenograft


E-MTAB-12238:Sample 94

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 94

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

characteristic: date

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: subclone

characteristic: time

text: Sample 94


E-MTAB-12238:Sample 95

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

text: E-MTAB-12238:Sample 95

text: Repli G

text: ArrayExpress

text: granulocyte monocyte progenitor cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38+, CD10-, CD7-, CD135(FLT3)+, CD45Ra+

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 95

text: 1:10 human CD45 positive out of mouse bone marrow 73


E-MTAB-12238:Sample 96

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 96

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: granulocyte monocyte progenitor cell

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

characteristic: date

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 96

characteristic: title

characteristic: xenograft


E-MTAB-12238:Sample 97

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

text: E-MTAB-12238:Sample 97

text: Repli G

text: ArrayExpress

text: hematopoietic multipotent progenitor cell

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: blood

characteristic: organism part

text: FACS Aria

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

characteristic: subclone

characteristic: time

text: Sample 97

text: 1:10 human CD45 positive out of mouse bone marrow 89


E-MTAB-12238:Sample 98

text: public

characteristic: SRA accession

text: E-MTAB-12238:Sample 98

characteristic: Submitter Id

text: Repli G

characteristic: WGA

text: ArrayExpress

characteristic: broker name

text: diagnosis

characteristic: clinical history

text: acute myeloid leukemia B phenotype

characteristic: clinical information

text: human

characteristic: common name

characteristic: date

characteristic: description

text: adult

characteristic: developmental stage

text: acute myeloid leukemia

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

text: FACS Aria

characteristic: protocol

characteristic: sample id

text: Homo sapiens

text: male

characteristic: sex

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 98


E-MTAB-12238:Sample 99

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

text: E-MTAB-12238:Sample 99

text: Repli G

text: ArrayExpress

text: diagnosis

text: acute myeloid leukemia B phenotype

text: human

text: adult

text: acute myeloid leukemia

characteristic: disease

text: CD34+, CD38-,CD90+/-, CD45Ra-

characteristic: immunophenotype

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone marrow

characteristic: organism part

text: FACS Aria - H4100 colony

text: Homo sapiens

text: male

text: BCR-ABL/NPM1-/FLT3 ITD-/DNMT3A-

text: Sample 99

characteristic: title


text: NIPH

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: S. pyogenes

characteristic: common name

text: GAS routine sample

characteristic: description

text: Norway

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Blood

text: Streptococcus pyogenes

text: Streptococcus pyogenes


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of South Bohemia

characteristic: INSDC center name

characteristic: INSDC first public

text: public

tag: Namespace:University of South Bohemia

text: microbiome in RAS biofiler

text: metagenome

text: metagenome

text: RAS biofilm metagenome


text: Institute of Cell Biology

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Institute of Cell Biology

text: Metabollic labelling of nascent transcripts

text: Trypanosoma brucei

characteristic: organism

text: Trypanosoma brucei

text: polyA selection from isolated nuclei (uninduced)


text: Institute of Cell Biology

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Trypanosoma brucei

text: Trypanosoma brucei

text: polyA selection from isolated nuclei (induced)

characteristic: title


text: SC

text: public

text: SC

characteristic: broker name

text: Rosalind Franklin Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Rosalind Franklin Laboratory by Donald Fraser, Suki Lee, Rob Howes, The Rosalind Franklin Laboratory and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team

characteristic: description

text: United Kingdom

text: Wales

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

text: active surveillance in response to outbreak

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: SC

text: Rosalind Franklin Laboratory

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: Scotland

text: Human

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: isolate


text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SC

characteristic: broker name

text: Lighthouse Lab in Glasgow

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Lighthouse Lab in Glasgow by Harper VanSteenhouse, Yumi Kasai, David Gray, Carol Clugston, Anna Dominiczak and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

text: Scotland

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: SC

text: Rosalind Franklin Laboratory

text: not provided

characteristic: description

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

text: Human

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: sample capture status


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: SC

text: Lighthouse Lab in Glasgow

text: not provided

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

text: Human

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

text: not provided

text: not provided

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: SC

characteristic: broker name

text: Lighthouse Laboratory Plymouth

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Samples prepared at Lighthouse Laboratory Plymouth by Lighthouse Laboratory Plymouth and Alex Alderton, Roberto Amato, Jeffrey Barrett, Sonia Goncalves, Ewan Harrison, David K. Jackson, Ian Johnston, Dominic Kwiatkowski, Cordelia Langford, John Sillitoe on behalf of the Wellcome Sanger Institute COVID-19 Surveillance Team (https://www.sanger.ac.uk/covid-team)

text: United Kingdom

text: England

text: Human

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

tag: Namespace:Dr. Risch

text: SIB

text: Dr. Risch Ostschweiz AG, Lagerstrasse 30, 9470 Buchs

text: Nadia Wohlwend, Faina Wehrli, Dominique Fabien Hilti, Sinem Kas, Martin Risch, Thomas Bodmer, Lorenz Risch

text: Liechtenstein

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Liechtenstein/FL-Risch-1018R14211/2022

characteristic: sample capture status

text: active surveillance not initiated by an outbreak


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Dr. Risch

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: Liechtenstein

characteristic: geographic location (country and/or sea)

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Liechtenstein/FL-Risch-1008R14256/2022

characteristic: isolate


characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Liechtenstein

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Liechtenstein/FL-Risch-1017R14210/2022

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

text: Switzerland

text: BE

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BE-Risch-1022R14259/2022

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: Liechtenstein

characteristic: geographic location (country and/or sea)

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Liechtenstein/FL-Risch-1006R14257/2022

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Dr. Risch

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

characteristic: broker name

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: GR

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/GR-Risch-1020R14280/2022

characteristic: organism

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: Dr. Risch

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: SIB

text: Liechtenstein

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Liechtenstein/FL-Risch-1003R14233/2022

characteristic: sample capture status


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text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-9121-7188/2022

characteristic: isolate


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: SIB

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-9118-7182/2022

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: GISAID Accession ID

characteristic: INSDC center name

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: SIB

text: Switzerland

text: BE

text: Human

characteristic: host common name

text: restricted access

text: Homo sapiens

text: restricted access

characteristic: host sex

text: restricted access

characteristic: host subject id

text: hCoV-19/Switzerland/BE-IFIK-9116-7177/2022

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: SIB

characteristic: broker name

text: Institute for Infectious Diseases, University of Bern, Switzerland

text: Lea Stauber, Christian Baumann, Miguel A Terrazos Miani, Sonja Gempeler, Loïc Borcard, Stefan Neuenschwander, Cora Sägesser, Pascal Bittel, Peter Keller, Franziska Suter-Riniker, Stephen L Leib, Alban Ramette

text: Switzerland

characteristic: geographic location (country and/or sea)

text: BE

characteristic: geographic location (region and locality)

text: Human

text: restricted access

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-9114-7165/2022

characteristic: isolate


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: GISAID Accession ID

text: Institute for Infectious Diseases, Bern, Switzerland

characteristic: INSDC center name

text: public

characteristic: INSDC status

text: SIB

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Switzerland

text: BE

text: Human

text: restricted access

text: Homo sapiens

text: restricted access

text: restricted access

text: hCoV-19/Switzerland/BE-IFIK-9127-7220/2022

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19524204 of study SRP378219.

characteristic: description

text: feces

characteristic: environmental medium

text: not provided

text: not provided

unit: DD

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Faecalibaculum rodentium

text: The goal of this study was to determine how age-related differences in gut metagenomes influenced the risk of sepsis in a mouse model

characteristic: project name

characteristic: sample derived from

text: Faecalibaculum rodentium

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Erysipelotrichia;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalibaculum;s__Faecalibaculum rodentium

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR19524204_bin.4_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: feces

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Clostridium sp.

characteristic: organism

text: uncultured Clostridium sp.

text: Illumina NovaSeq 6000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR19524204_bin.6_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: not provided

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Alistipes sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Alistipes sp.

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR19524204_bin.7_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19524205 of study SRP378219.

text: feces

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Coriobacteriaceae bacterium

characteristic: organism

text: uncultured Coriobacteriaceae bacterium

text: Illumina NovaSeq 6000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR19524205_bin.3_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: not provided

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Porphyromonadaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Porphyromonadaceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Porphyromonadaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR19524205_bin.4_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19524206 of study SRP378219.

text: feces

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Porphyromonadaceae bacterium

characteristic: organism

text: uncultured Porphyromonadaceae bacterium

text: Illumina NovaSeq 6000

text: multi-marker approach

text: Metagenome-assembled genome: SRR19524206_bin.5_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Many fragments with little to no review of assembly other than reporting of standard assembly statistics

text: metaSPAdes v3.15.3

text: metawrap v1.3

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: feces

characteristic: environmental medium

text: not provided

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: Bifidobacterium pseudolongum

characteristic: project name

characteristic: sample derived from

text: Bifidobacterium pseudolongum

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Actinobacteria;c__Actinobacteria;o__Bifidobacteriales;f__Bifidobacteriaceae;g__Bifidobacterium;s__Bifidobacterium pseudolongum

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR19524206_bin.7_metawrap_v1.3_MAG


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: EMG

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaSPAdes v3.15.3

characteristic: assembly software

text: MaxBin2, MetaBat2, Concoct with default parameter of the metaWRAP pipeline. Bin refinement module used from metaWRAP with default parameters.

characteristic: binning parameters

text: metawrap v1.3

characteristic: binning software

text: mouse digestive system

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19524208 of study SRP378219.

text: feces

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

text: not provided

text: metagenome-assembled genome

text: mouse gut metagenome

text: digestive tube

text: mouse gut metagenome

text: uncultured Eubacterium sp.

characteristic: organism

text: The goal of this study was to determine how age-related differences in gut metagenomes influenced the risk of sepsis in a mouse model

text: uncultured Eubacterium sp.

text: Illumina NovaSeq 6000

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Eubacteriaceae;g__Eubacterium;s__

text: multi-marker approach

text: Metagenome-assembled genome: SRR19524208_bin.2_metawrap_v1.3_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: metaSPAdes v3.15.3

text: metawrap v1.3

text: mouse digestive system

characteristic: broad-scale environmental context

text: EBI-EMG

text: not provided

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run SRR19524209 of study SRP378219.

characteristic: description

text: feces

characteristic: environmental medium

text: not provided

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

characteristic: investigation type

text: mouse gut metagenome

text: digestive tube

characteristic: local environmental context

text: mouse gut metagenome

characteristic: metagenomic source

text: uncultured Muribaculaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Muribaculaceae bacterium

text: Illumina NovaSeq 6000

characteristic: sequencing method

text: The taxonomy of this metagenome-assembled genome was originally computed with GTDBtk, which assigned the following taxonomic annotation: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__;s__

characteristic: taxonomic classification

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: SRR19524209_bin.2_metawrap_v1.3_MAG