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text: Verena Kufner, Maryam Zaheri, Stefan Schmutz, Kevin Steiner, Riccarda Capaul, Guido Bloemberg, Michael Huber, Alexandra Trkola, Christian Beisel, Tobias Schär, Ina Nissen, Natascha Santacroce, Rebecca Denes, Mirjam Feldkamp, Elodie Burcklen, Chaoran Chen, Sarah Nadeau, Louis du Plessis, Ivan Topolsky, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Pelin Burcak Icer, Matteo Carrara, Shuqing Yu, Franziska Singer, Niko Beerenwinkel, Tanja Stadler

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text: Spina Valeria Romina, Gloria Gaudio, Gladys Martinetti Lucchini, Christian Beisel, Tobias Schär, Ina Nissen, Natascha Santacroce, Rebecca Denes, Mirjam Feldkamp, Elodie Burcklen, Chaoran Chen, Sarah Nadeau, Louis du Plessis, Ivan Topolsky, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Pelin Burcak Icer, Matteo Carrara, Shuqing Yu, Franziska Singer, Niko Beerenwinkel, Tanja Stadler

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text: Spina Valeria Romina, Gloria Gaudio, Gladys Martinetti Lucchini, Christian Beisel, Tobias Schär, Ina Nissen, Natascha Santacroce, Rebecca Denes, Mirjam Feldkamp, Elodie Burcklen, Chaoran Chen, Sarah Nadeau, Louis du Plessis, Ivan Topolsky, Kim Philipp Jablonski, Lara Fuhrmann, David Dreifuss, Pelin Burcak Icer, Matteo Carrara, Shuqing Yu, Franziska Singer, Niko Beerenwinkel, Tanja Stadler

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text: Switzerland

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tag: Namespace:UNIVERSITY OF OSLO

characteristic: description

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characteristic: geographic location (country and/or sea)

text: mycobacterium tuberculosis

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text: genome

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: Kathrine Stene-Johansen, Kamilla Heddeland Instefjord, Hilde Elshaug, Garcia Llorente Ignacio, Jon Bråte, Engebretsen Serina Beate, Pedersen Benedikte Nevjen, Line Victoria Moen, Hilde Nordby Falkenhaug, Debech Nadia, Atiya R Ali, Marie Paulsen Madsen, Rasmus Riis Kopperud, Hilde Vollan, Karoline Bragstad, Olav Hungnes

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tag: Namespace:Norwegian Institute of Public Health (NIPH)

text: ELIXIR-Norway

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text: not provided

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characteristic: collection date

text: not provided

text: Norway

text: More og Romsdal

text: Human

text: not provided

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text: not provided

text: not provided

text: not provided

text: Severe acute respiratory syndrome coronavirus 2


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text: Hospital of Southern Norway - Kristiansand, Department of Medical Microbiology ; P.O.Box 416 Lundsiden, N-4604 Kristiansand, Norway

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text: Norway

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text: Innlandet Hospital Trust, Division Lillehammer, Department for Medical Microbiology ; P.O.Box 990, N-2629 Lillehammer, Norway

characteristic: collecting institution

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characteristic: geographic location (country and/or sea)

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text: not provided

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characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Vestland

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: Authors

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Nordland Hospital - Bodo, Laboratory Department, Molecular Biology Unit ; P.O.Box 1480, N-8092 Bodo, Norway

text: not provided

text: Norway

text: Nordland

text: Human

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: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ELIXIR-Norway

characteristic: broker name

text: University Hospital of Northern Norway, Department for Microbiology and Infectious Disease Control ; P.O.Box 56, N-9038 Tromsoe, Norway

text: not provided

text: Norway

text: Troms og Finnmark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

characteristic: organism

characteristic: title


characteristic: Authors

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Ostfold Hospital Trust - Kalnes, Centre for Laboratory Medicine, Section for gene technology and infection serology ; P.O.Box 300, N-1714 Graalum, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Viken

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

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

text: public

text: ELIXIR-Norway

text: Haugesund Hospital, laboratory for Medical Microbiology ; P.O.Box 2170, N-5504 Haugesund, Norway

text: not provided

text: Norway

text: Rogaland

text: Human

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


text: School of medicine, Tongji University

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:School of medicine, Tongji University

characteristic: Submitter Id

text: HepG2 cell

text: human

characteristic: common name

text: nanopore sequencing reads from nanoHiMe-seq experiment

characteristic: description

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: H3K27me3 nanoHiMe-seq sample

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: H3K4me3 nanoHiMe-seq sample


characteristic: External Id

text: School of medicine, Tongji University

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: HepG2 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: IgG nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: GM12878 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: GM12878_EPZ6438_treated_nanoHiMe_H3K27me3_1

text: GM12878 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: GM12878_EPZ6438_treated_nanoHiMe_H3K27me3_2

text: GM12878 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: GM12878_EPZ6438_treated_nanoHiMe_H3K27me3_3

text: GM12878 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: GM12878 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: IgG nanoHiMe-seq sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: nanopore sequencing reads of genomic DNA amplicons

text: Homo sapiens

text: Homo sapiens

text: Sample of genomic DNA amplicons


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: nanopore sequencing reads of genomic DNA amplicons treated with methyltransferases

text: Homo sapiens

text: Homo sapiens

text: Sample of genomic DNA amplicons treated with M.SssI


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Sample of genomic DNA amplicons treated with pA-Hia5


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: Sample of genomic DNA amplicons treated with both M.SssI and pA-Hia5


text: School of medicine, Tongji University

text: public

text: Escherichia coli str. K-12 substr. MG1655

text: E.coli MG1655

characteristic: strain

text: Sample of genomic DNA amplicons


text: School of medicine, Tongji University

text: public

text: E.coli MG1655


text: School of medicine, Tongji University

text: public

text: E.coli MG1655


text: School of medicine, Tongji University

text: public

text: E.coli MG1655


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Illumina reads from CUT&Tag experiment

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 CUT-Tag sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Illumina reads from CUT&Tag experiment

text: Homo sapiens

text: Homo sapiens

text: H3K4me3 CUT-Tag sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Illumina reads from CUT&Tag experiment

text: Homo sapiens

text: Homo sapiens

text: IgG CUT-Tag sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Illumina reads from CUT&Tag-BS experiment

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 CUT-Tag-BS sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Illumina reads from CUT&Tag-noBS experiment

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 CUT-Tag-noBS sample


text: School of medicine, Tongji University

text: public

text: HepG2 cell

text: human

text: Homo sapiens

text: Homo sapiens

text: IgG CUT-Tag-noBS sample


text: School of medicine, Tongji University

text: public

text: GM12878 cell

text: human

text: Illumina reads from CUT&Tag experiment

text: Homo sapiens

text: Homo sapiens

text: H3K27me3 CUT-Tag sample


text: School of medicine, Tongji University

text: public

text: GM12878 cell

text: human

text: Illumina reads from CUT&Tag experiment

text: Homo sapiens

text: Homo sapiens

text: IgG CUT-Tag sample


text: INRA-META

text: public

text: Denmark

characteristic: geographic location (country and/or sea)

text: stool

characteristic: host body product

text: human-gut

characteristic: host body site

text: human gut metagenome

text: human gut metagenome

text: human gut metagenome


text: Kathrine Stene-Johansen, Kamilla Heddeland Instefjord, Hilde Elshaug, Garcia Llorente Ignacio, Jon Bråte, Engebretsen Serina Beate, Pedersen Benedikte Nevjen, Line Victoria Moen, Hilde Nordby Falkenhaug, Debech Nadia, Atiya R Ali, Marie Paulsen Madsen, Rasmus Riis Kopperud, Hilde Vollan, Karoline Bragstad, Olav Hungnes

characteristic: Authors

characteristic: GISAID Accession ID

text: Norwegian Institute of Public Health (NIPH)

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

characteristic: broker name

text: Haukeland University Hospital, Dept. of Microbiology ; P.O.Box 1400, N-5021 Bergen, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

text: Vestland

characteristic: geographic location (region and locality)

text: Human

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

characteristic: isolate

text: not provided

characteristic: isolation source host-associated

text: Severe acute respiratory syndrome coronavirus 2


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Vestfold Hospital, Toensberg, Department of Microbiology ; P.O.Box 2168, N-3103 Toensberg, Norway

text: not provided

text: Norway

characteristic: geographic location (country and/or sea)

text: Vestfold og Telemark

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


characteristic: Authors

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ELIXIR-Norway

characteristic: broker name

text: Department of Medical Microbiology - section Molde, Molde Hospital ; Parkveien 84, N-6407 Molde, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

text: More og Romsdal

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

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

text: public

text: ELIXIR-Norway

text: Hospital of Southern Norway - Kristiansand, Department of Medical Microbiology ; P.O.Box 416 Lundsiden, N-4604 Kristiansand, Norway

text: not provided

text: Norway

text: Agder

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated


characteristic: Authors

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

characteristic: broker name

text: Medical Microbiology Unit, Department for Laboratory Medicine, Drammen Hospital, Vestre Viken Health Trust ; P.O.Box 800, N-3004 Drammen, Norway

characteristic: collecting institution

text: not provided

text: Norway

characteristic: geographic location (country and/or sea)

text: Viken

text: Human

text: not provided

text: Homo sapiens

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

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ELIXIR-Norway

text: Innlandet Hospital Trust, Division Lillehammer, Department for Medical Microbiology ; P.O.Box 990, N-2629 Lillehammer, Norway

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

text: Innlandet

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: Authors

characteristic: GISAID Accession ID

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ELIXIR-Norway

text: Foerde Hospital, Department of Microbiology ; P.O.Box 1000, N-6807 Foerde, Norway

text: not provided

text: Norway

text: Vestland

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

characteristic: isolate

text: not provided

characteristic: isolation source host-associated


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ELIXIR-Norway

characteristic: broker name

text: Haugesund Hospital, laboratory for Medical Microbiology ; P.O.Box 2170, N-5504 Haugesund, Norway

characteristic: collecting institution

text: not provided

text: Norway

characteristic: geographic location (country and/or sea)

text: Rogaland

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: organism

characteristic: title


text: Chongqing University Cancer Hospital

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Chongqing University Cancer Hospital

characteristic: Submitter Id

text: Yes

characteristic: Was the PDX model humanised?

text: human

characteristic: common name

text: primary cancer

characteristic: description

text: tumor

characteristic: engrafted tumor collection site

characteristic: engrafted tumor sample passage

characteristic: engraftment host strain name

text: Homo sapiens

text: not provided

characteristic: patient age at collection of tumor

text: Female

characteristic: patient sex

characteristic: patient tumor diagnosis at time of collection

text: Primary Neoplasm

characteristic: patient tumor type

text: tissue fragment

characteristic: sample material

text: Patient tumor

characteristic: sample origin

text: Homo sapiens

characteristic: sample taxon name

characteristic: sample unique ID

text: Homo sapiens

text: breast cancer


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

tag: Namespace:The Johns Hopkins Kimmel Comprehensive Cancer Center

text: HLA A3 SLISY run corresponding to Fig 1C

text: Escherichia phage M13

characteristic: organism

text: Escherichia phage M13

characteristic: title


text: The Johns Hopkins Kimmel Comprehensive Cancer Center

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: description

text: Escherichia phage M13

text: Escherichia phage M13


text: public

text: SARS-CoV-2 SLISY run corresponding to Fig 2C 2D 3D 3E

text: Escherichia phage M13

text: Escherichia phage M13


text: public

text: SARS-CoV-2 SLISY run corresponding to Fig 3A

text: Escherichia phage M13

text: Escherichia phage M13


text: public

text: SARS-CoV-2 SLISY run corresponding to Fig 5A 5B 6A Supp Fig 5

text: Escherichia phage M13

text: Escherichia phage M13


text: public

text: SARS-CoV-2 SLISY run corresponding to Fig 6A

text: Escherichia phage M13

text: Escherichia phage M13


text: Shanghai Tenth People's Hospital

text: public

tag: Namespace:Shanghai Tenth People's Hospital

text: ArrayExpress

characteristic: broker name

text: Protocols: Cells were grown in YPD broth at 37˚C from OD600=0.01 till OD600=1.0. Cells were treated with 0.5 µg/ml or 8 µg/ml of tunicamycin, or DMSO (control) for 3h. Pellets of 5ml cell culture were obtained by centrifuging at maximum speed for 1min. the pellets were fast frozen in liquid nitrogen. RNA was extracted using the TRIzol method following the manufacturer's protocol. Cell pellets were transferred from liquid nitrogen into the 2ml tub containing 1.5ml Trizol reagent. The mix was shared for 3min, and kept for 5in at room temperature, then centrifuged at 10,000xg for 5min at 4˚C. The supernatant was added 200µl of chloroform/isoamyl alcohol (24:1) with 1ml lysis reagents. After centrifuged at 10,000g for 10min at 4˚C, the supernatant was transferred into another new tube with equal volume of isopropanol and put in the refrigerator at -20˚C for 1h. After centrifuged at 13600xg for 20min at 4˚C, the supernatant was precipitated by 1ml of 75% ethanol and let dry for 3-5min. The RNA pellet was dissolved with 30-100µl of DEPC water. The concentration of the extracted RNA was determined using a Nanodrop system (NanoDrop, Madison, USA), and the integrity of the RNA was examined by the RNA integrity number (RIN) using an Agilent 2100 bioanalyzer (Agilent, Santa Clara, USA) buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library.

text: log phase

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

text: YPD broth

characteristic: growth condition

characteristic: individual

text: [Candida] glabrata

text: [Candida] glabrata

text: whole organism

characteristic: organism part

text: [Candida] glabrata

characteristic: strain


text: Kathrine Stene-Johansen, Kamilla Heddeland Instefjord, Hilde Elshaug, Garcia Llorente Ignacio, Jon Bråte, Engebretsen Serina Beate, Pedersen Benedikte Nevjen, Line Victoria Moen, Hilde Nordby Falkenhaug, Debech Nadia, Atiya R Ali, Marie Paulsen Madsen, Rasmus Riis Kopperud, Hilde Vollan, Karoline Bragstad, Olav Hungnes

characteristic: Authors

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: GISAID Accession ID

text: Norwegian Institute of Public Health (NIPH)

text: public

text: ELIXIR-Norway

text: Dept. of Medical Microbiology, Stavanger University Hospital, Helse Stavanger HF ; P.O.Box 8100, N-4068 Stavanger, Norway

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Norway

characteristic: geographic location (country and/or sea)

text: Rogaland

characteristic: geographic location (region and locality)

text: Human

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

characteristic: isolate

text: not provided

characteristic: isolation source host-associated