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text: Aare Abroi, Radko Avi, Taavi Päll, Heiki Niglas , Merit Pauskar, Arina Shablinskaja, Eveli Kallas, Andrio Lahesaare, Kai Truusalu, Dagmar Hoidmets, Olga Sadikova, Kaspar Ratnik, Hanna Sepp, Liidia Dotsenko, Jevgenia Epštein, Heleene Suija, Katrin Kaarna, Lili Milani, Mait Metspalu, Ott Eric Oopkaup, Ivar Koppel, Erik Jaaniso, Ivan Kuzmin, Uku Raudvere, Tuuli Reisberg, Hedi Peterson, Ulvi Gerst Talas, Paul Naaber, Mari-Anne Härma, Irja Lutsar, Kristi Huik

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text: Lighthouse Lab in Glasgow

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)

characteristic: description

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

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text: Lighthouse Lab in Milton Keynes

characteristic: collecting institution

characteristic: collection date

text: Samples prepared at Lighthouse Lab in Milton Keynes by The Lighthouse Lab in Milton Keynes 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

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characteristic: External Id

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text: Lighthouse Lab in Alderley Park

text: Samples prepared at Lighthouse Lab in Alderley Park by Jacquelyn Wynn, Mairead Hyland, The Lighthouse Lab in Alderley Park 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

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text: Scotland

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text: Integrated Covid Hub North East

text: Samples prepared at Integrated Covid Hub North East by Integrated Covid Hub North East 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

text: United Kingdom

text: England

text: Human


text: SC

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characteristic: Submitter Id

text: SC

text: Lighthouse Lab in Alderley Park

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text: England

text: Human

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characteristic: sample capture status

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characteristic: ENA-LAST-UPDATE

text: SC

text: public

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text: Rosalind Franklin Laboratory

characteristic: collecting institution

characteristic: collection date

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

text: United Kingdom

text: England

text: Human

characteristic: host scientific name


E-MTAB-5742:Sample 1(SCI045144-1)

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text: UNIVERSITY OF NEW MEXICO

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text: public

text: E-MTAB-5742:Sample 1(SCI045144-1)

tag: Namespace:UNIVERSITY OF NEW MEXICO

text: ArrayExpress

text: microglial cell

characteristic: cell type

text: human

characteristic: common name

text: Protocols: Human microglial cells (ScienCell, Cat. #: 1900) were thawed and plated in a 6-well tissue culture plate pre-coated with 0.1mg/ml of Poly-L-Lysine (Sigma, P4707). The culture media was changed 16 hours after thawing and cells remained undisturbed for another 24hours. Human microglial cells were treated with vehicle or 2ug/ml of hPHF (paired helical filaments isolated from human AD brain) in triplicates for 24 hours. RNA was extracted from cells using Qiagen Rneasy mini kit with DNase treatment as per manufacturer's instructions. Library construction was performed by Quick Biology Inc. (Pasadena, CA) using KAPA Stranded RNA-Seq Kits with RiboErase.

text: normal

characteristic: disease

text: Homo sapiens

text: Homo sapiens

text: brain

characteristic: organism part

text: Homo sapiens

text: Sample 1(SCI045144-1)


E-MTAB-5742:Sample 2(SCI045144-2)

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text: UNIVERSITY OF NEW MEXICO

text: public

characteristic: INSDC status

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text: E-MTAB-5742:Sample 2(SCI045144-2)

text: ArrayExpress

characteristic: broker name

text: microglial cell

text: human

characteristic: description

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 2(SCI045144-2)


E-MTAB-5742:Sample 3(SCI045144-3)

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text: UNIVERSITY OF NEW MEXICO

text: public

text: E-MTAB-5742:Sample 3(SCI045144-3)

characteristic: Submitter Id

text: ArrayExpress

text: microglial cell

text: human

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 3(SCI045144-3)

characteristic: title


E-MTAB-5742:Sample 4(SCI045144-4)

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text: UNIVERSITY OF NEW MEXICO

characteristic: INSDC center name

text: public

text: E-MTAB-5742:Sample 4(SCI045144-4)

text: ArrayExpress

text: microglial cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 4(SCI045144-4)


E-MTAB-5742:Sample 5(SCI045144-5)

text: UNIVERSITY OF NEW MEXICO

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5742:Sample 5(SCI045144-5)

text: ArrayExpress

text: microglial cell

text: human

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 5(SCI045144-5)


E-MTAB-5742:Sample 6(SCI045144-6)

text: UNIVERSITY OF NEW MEXICO

text: public

text: E-MTAB-5742:Sample 6(SCI045144-6)

text: ArrayExpress

text: microglial cell

characteristic: cell type

text: human

characteristic: common name

text: normal

text: Homo sapiens

text: Homo sapiens

text: brain

text: Homo sapiens

text: Sample 6(SCI045144-6)


text: University of Tartu, Estonia

text: public

text: ena-upload-cli v0.3.1 @ Galaxy

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: human

characteristic: host common name

text: healthy

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: host subject id

characteristic: host subject id

characteristic: isolate

characteristic: isolation source non-host-associated

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Tartu, Estonia

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-upload-cli v0.3.1 @ Galaxy

characteristic: Submitter Id

characteristic: description

text: Estonia

text: human

text: diseased

text: Homo sapiens

text: male

text: host subject id

characteristic: organism

characteristic: title


text: University of Tartu, Estonia

text: public

text: ena-upload-cli v0.3.1 @ Galaxy

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

text: Estonia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: human

characteristic: host common name

text: healthy

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: host subject id

characteristic: host subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Tartu, Estonia

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ena-upload-cli v0.3.1 @ Galaxy

text: Estonia

text: human

text: diseased

text: Homo sapiens

text: female

text: host subject id

characteristic: isolate

characteristic: isolation source non-host-associated

characteristic: sample capture status


text: University of Tartu, Estonia

text: public

text: ena-upload-cli v0.3.1 @ Galaxy

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

characteristic: collector name

characteristic: description

text: Estonia

characteristic: geographic location (country and/or sea)

text: human

characteristic: host common name

text: not provided

text: Homo sapiens

text: male

text: host subject id

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: University of Tartu, Estonia

characteristic: INSDC center name

text: public

text: ena-upload-cli v0.3.1 @ Galaxy

text: Estonia

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

characteristic: host age

text: human

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: host subject id

characteristic: host subject id


text: EMG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

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: Flye Assembler v. 2.4.2

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 v1.1

characteristic: binning software

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

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 DRR214961 of study DRP005925.

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: uncultured Actinomyces sp.

text: >30Gb sequence data per sample were generated for joint analysis of > 30Gb long read sequence data of PromethION (JGAS00000000186 in JGA database) The Data Access Committee of the National Bioscience Database Center (NBDC) approved that this personal genetic data were made published according to NBDC data sharing guidelines (http://humandbs.biosciencedbc.jp/).

characteristic: project name

characteristic: sample derived from

text: uncultured Actinomyces sp.

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214961_bin.28_metaWRAP_v1.1_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: Flye Assembler v. 2.4.2

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

text: not provided

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run DRR214962 of study DRP005925.

text: Human oral metagenome

text: Human oral cavity

text: Saliva

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human saliva metagenome

text: human saliva metagenome

text: uncultured Solobacterium sp.

characteristic: organism

text: uncultured Solobacterium sp.

text: HiSeq X Ten

text: multi-marker approach

text: Metagenome-assembled genome: DRR214962_bin.34_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S, and 5S rRNA genes and at least 18 tRNAs

text: Flye Assembler v. 2.4.2

text: metaWRAP v1.1

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

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 DRR214959 of study DRP005925.

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: uncultured Atopobium sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Atopobium sp.

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214959_bin.32_metaWRAP_v1.1_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: Flye Assembler v. 2.4.2

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

text: not provided

text: CheckM

text: Human oral metagenome

text: Human oral cavity

text: Saliva

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human saliva metagenome

text: human saliva metagenome

text: uncultured Prevotellaceae bacterium

characteristic: organism

text: uncultured Prevotellaceae bacterium

text: HiSeq X Ten

text: multi-marker approach

text: Metagenome-assembled genome: DRR214961_bin.6_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Flye Assembler v. 2.4.2

text: metaWRAP v1.1

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: uncultured Prevotellaceae bacterium

characteristic: project name

characteristic: sample derived from

text: uncultured Prevotellaceae bacterium

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214961_bin.19_metaWRAP_v1.1_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: Flye Assembler v. 2.4.2

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

text: not provided

text: CheckM

text: This sample represents a Third Party Annotation (TPA) Metagenome-Assembled Genome (MAG) assembled from the metagenomic run DRR214960 of study DRP005925.

text: Human oral metagenome

text: Human oral cavity

text: Saliva

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human saliva metagenome

text: human saliva metagenome

text: Mogibacterium diversum

characteristic: organism

text: Mogibacterium diversum

text: HiSeq X Ten

text: multi-marker approach

text: Metagenome-assembled genome: DRR214960_bin.7_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Flye Assembler v. 2.4.2

text: metaWRAP v1.1

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: uncultured Stomatobaculum sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Stomatobaculum sp.

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214959_bin.22_metaWRAP_v1.1_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: Flye Assembler v. 2.4.2

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

text: not provided

text: CheckM

text: Human oral metagenome

text: Human oral cavity

text: Saliva

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human saliva metagenome

text: human saliva metagenome

text: uncultured Oribacterium sp.

characteristic: organism

text: uncultured Oribacterium sp.

text: HiSeq X Ten

text: multi-marker approach

text: Metagenome-assembled genome: DRR214960_bin.11_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Flye Assembler v. 2.4.2

text: metaWRAP v1.1

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: uncultured Actinomyces sp.

characteristic: project name

characteristic: sample derived from

text: uncultured Actinomyces sp.

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214962_bin.12_metaWRAP_v1.1_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

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

characteristic: assembly quality

text: Flye Assembler v. 2.4.2

characteristic: assembly software

characteristic: binning parameters

text: metaWRAP v1.1

characteristic: binning software

text: EBI-EMG

text: not provided

text: CheckM

text: Human oral metagenome

text: Human oral cavity

text: Saliva

text: not provided

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: geographic location (latitude)

text: not provided

characteristic: geographic location (longitude)

text: metagenome-assembled genome

text: human saliva metagenome

text: human saliva metagenome

text: uncultured Catonella sp.

characteristic: organism

text: uncultured Catonella sp.

text: HiSeq X Ten

text: multi-marker approach

text: Metagenome-assembled genome: DRR214959_bin.5_metaWRAP_v1.1_MAG

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: EMG

text: public

text: Flye Assembler v. 2.4.2

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

text: metaWRAP v1.1

text: EBI-EMG

characteristic: broker name

text: not provided

characteristic: collection date

characteristic: completeness score

text: CheckM

characteristic: completeness software

characteristic: contamination score

characteristic: description

text: Human oral metagenome

characteristic: environment (biome)

text: Human oral cavity

characteristic: environment (feature)

text: Saliva

characteristic: environment (material)

text: not provided

text: not provided

text: not provided

text: metagenome-assembled genome

characteristic: investigation type

text: human saliva metagenome

characteristic: isolation source

text: human saliva metagenome

characteristic: metagenomic source

text: Corynebacterium freiburgense

characteristic: project name

characteristic: sample derived from

text: Corynebacterium freiburgense

text: HiSeq X Ten

characteristic: sequencing method

text: multi-marker approach

characteristic: taxonomic identity marker

text: Metagenome-assembled genome: DRR214959_bin.2_metaWRAP_v1.1_MAG