text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: completeness score

text: checkM (version 1.2.1); checkM_DB (release 2015-01-16)

characteristic: completeness software

characteristic: contamination score

text: adult sponge tissue

characteristic: environmental medium

text: Portugal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pedra da Greta

text: Coastal Seawater

text: adult

text: Sarcotragus spinosulus

text: JORGE GONÇALVES

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

characteristic: investigation type

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

characteristic: local environmental context

text: sponge metagenome

characteristic: metagenomic source

characteristic: number of standard tRNAs extracted

text: Arenicellales bacterium

text: WHOLE ORGANISM

text: ASG

characteristic: project name

text: Heterotrophic Microbiome (Mostly)

text: Arenicellales bacterium

text: Pacbio Sequel II

characteristic: sequencing method

text: NOT PROVIDED

text: PROKKA (version 1.14.5)

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: taxonomic classification fully defined by topology

characteristic: taxonomic identity marker

text: a29debac-1c8f-4757-9535-86e5a3768f11-asg-MAGScoT_cleanbin_000009


status: PUBLIC

text: Yes

tag: attribute

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

tag: Namespace:Tree of Life Programme

characteristic: Submitter Id

text: Single contiguous sequence without gaps or ambiguities with a consensus error rate equivalent to Q50 or better

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

text: MAGScoT (version 1.0.0); MetaBat (version 2.15-15-gd6ea400); bin3C (version 0.3.3); MaxBin (version 2.7); MetaTOR

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: collected by

text: UNIVERSITY OF LISBON AND CENTRE OF MARINE SCIENCES

characteristic: collecting institution

characteristic: collection date

unit: m

characteristic: depth

text: adult sponge tissue

text: Portugal

unit: DD

text: Pedra da Greta

characteristic: geographic location (region and locality)

text: Coastal Seawater

characteristic: habitat

text: adult

characteristic: host life stage

text: Sarcotragus spinosulus

characteristic: host scientific name

characteristic: host taxid

text: JORGE GONÇALVES

characteristic: identified by

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

text: sponge metagenome

text: Arenicellales bacterium

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: ASG

text: Heterotrophic Microbiome (Mostly)

characteristic: relationship

characteristic: sample derived from

text: Arenicellales bacterium

text: Pacbio Sequel II

characteristic: specimen id

text: NOT PROVIDED

characteristic: specimen voucher

text: PROKKA (version 1.14.5)

text: GTDB-TK (version 2.1.1); GTDB (release 207_v2)

text: 614c4e07-9228-4473-aec8-20aab4a72dbc-asg-MAGScoT_cleanbin_000015


text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: adult sponge tissue

characteristic: environmental medium

text: Portugal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pedra da Greta

text: Coastal Seawater

text: adult

text: Sarcotragus spinosulus

text: JORGE GONÇALVES

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

characteristic: investigation type

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

characteristic: local environmental context

text: sponge metagenome

characteristic: metagenomic source

characteristic: number of standard tRNAs extracted

text: Arenicellales bacterium

text: WHOLE ORGANISM

text: ASG

characteristic: project name

text: Heterotrophic Microbiome (Mostly)

text: Arenicellales bacterium

text: Pacbio Sequel II

characteristic: sequencing method

text: NOT PROVIDED

text: PROKKA (version 1.14.5)

characteristic: tRNA extraction software

characteristic: taxonomic classification

text: taxonomic classification defined by topology and ANI

characteristic: taxonomic identity marker

text: a9d0d3a5-81af-420e-bf60-509b1b1d7e24-asg-MAGScoT_cleanbin_000004


text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: collected by

characteristic: collecting institution

characteristic: collection date

characteristic: depth

text: adult sponge tissue

text: Portugal

text: Pedra da Greta

characteristic: geographic location (region and locality)

text: Coastal Seawater

characteristic: habitat

text: adult

characteristic: host life stage

text: Sarcotragus spinosulus

characteristic: host scientific name

characteristic: host taxid

text: JORGE GONÇALVES

characteristic: identified by

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

text: sponge metagenome

text: Gammaproteobacteria bacterium

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: ASG

text: Heterotrophic Microbiome (Mostly)

characteristic: relationship

characteristic: sample derived from

text: Gammaproteobacteria bacterium

text: Pacbio Sequel II

characteristic: specimen id

text: NOT PROVIDED

characteristic: specimen voucher

text: PROKKA (version 1.14.5)

text: 81158527-d3f1-4143-94c3-cdad33fa9801-asg-MAGScoT_cleanbin_000034


text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: adult sponge tissue

characteristic: environmental medium

text: Portugal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pedra da Greta

text: Coastal Seawater

text: adult

text: Sarcotragus spinosulus

text: JORGE GONÇALVES

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

characteristic: investigation type

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

characteristic: local environmental context

text: sponge metagenome

characteristic: metagenomic source

characteristic: number of standard tRNAs extracted

text: Gammaproteobacteria bacterium

text: WHOLE ORGANISM

text: ASG

characteristic: project name

text: Heterotrophic Microbiome (Mostly)

text: Gammaproteobacteria bacterium

text: Pacbio Sequel II

characteristic: sequencing method

text: NOT PROVIDED

text: PROKKA (version 1.14.5)

characteristic: tRNA extraction software

characteristic: taxonomic classification

characteristic: taxonomic identity marker

text: 1edb315a-a588-40c5-a4bd-ab3494138ff0-asg-MAGScoT_cleanbin_000028


text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: collected by

characteristic: collecting institution

characteristic: collection date

characteristic: depth

text: adult sponge tissue

text: Portugal

text: Pedra da Greta

characteristic: geographic location (region and locality)

text: Coastal Seawater

characteristic: habitat

text: adult

characteristic: host life stage

text: Sarcotragus spinosulus

characteristic: host scientific name

characteristic: host taxid

text: JORGE GONÇALVES

characteristic: identified by

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

text: sponge metagenome

text: Spirochaetia bacterium

characteristic: organism

text: WHOLE ORGANISM

characteristic: organism part

text: ASG

text: Heterotrophic Microbiome (Mostly)

characteristic: relationship

characteristic: sample derived from

text: Spirochaetia bacterium

text: Pacbio Sequel II

characteristic: specimen id

text: NOT PROVIDED

characteristic: specimen voucher

text: PROKKA (version 1.14.5)

text: taxonomic novelty determined using RED

text: 186bcdf5-c437-4417-98ce-b40e47850191-asg-MAGScoT_cleanbin_000047


text: Yes

characteristic: 16S recovered

text: PROKKA (version 1.14.5)

characteristic: 16S recovery software

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Geomar Helmholtz Centre

characteristic: GAL

text: NOT PROVIDED

text: Tree of Life Programme

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Minimap2 (version 2.24-r1122)

characteristic: MAG coverage software

characteristic: SRA accession

characteristic: Submitter Id

characteristic: assembly quality

text: metaMDBG

characteristic: assembly software

text: coverage; graph; hic-mapping

characteristic: binning parameters

characteristic: binning software

text: aquatic biome

characteristic: broad-scale environmental context

text: RODRIGO COSTA

characteristic: completeness score

characteristic: completeness software

characteristic: contamination score

text: adult sponge tissue

characteristic: environmental medium

text: Portugal

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Pedra da Greta

text: Coastal Seawater

text: adult

text: Sarcotragus spinosulus

text: JORGE GONÇALVES

text: CENTRE OF MARINE SCIENCES

text: metagenome-assembled genome

characteristic: investigation type

text: Sponge: Sarcotragus spinosulus

text: marine benthic biome

characteristic: local environmental context

text: sponge metagenome

characteristic: metagenomic source

characteristic: number of standard tRNAs extracted

text: bacterium

text: WHOLE ORGANISM

text: ASG

characteristic: project name

text: Heterotrophic Microbiome (Mostly)

text: bacterium

text: Pacbio Sequel II

characteristic: sequencing method

text: NOT PROVIDED

text: PROKKA (version 1.14.5)

characteristic: tRNA extraction software

characteristic: taxonomic classification

characteristic: taxonomic identity marker

text: bb12cdae-2636-4da8-858f-c18d35c17727-asg-MAGScoT_cleanbin_000060


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Latvian Biomedical Research and Study Centre

characteristic: Submitter Id

characteristic: collection date

text: human

characteristic: common name

text: CYP2E1 library

characteristic: description

text: Latvia

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: Whole Blood DNA

characteristic: title


text: Latvian Biomedical Research and Study Centre

text: public

text: human

text: CYP2E1 library

text: Latvia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

text: Homo sapiens

text: Whole Blood DNA


text: BIMSB

text: public

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: Protocols: Cells from a 90% confluent 10 cm dish were harvested and counted, 8 million cells were mixed with 2 million Drosophila S2 cells as a spike-in control. Cell pellets from one well on a 6-well plate were resuspended in 1 mL TRI reagent (Sigma) and incubated for 5 min at room temperature. 200 µL chloroform (Applichem) was added and the lysate was vortexed and centrifuged at max. speed (21130g) for 15 min at 4°C. The aqueous layer was transferred to a new tube and precipitated with 0.5 mL isopropanol. The RNA pellet was isolated by centrifugation for 30 min at 4°C, washed with 1 mL 75% ethanol, re-centrifuged for 10 min, dried and resuspended in 70 µL RNase free water. 20 µg RNA was treated with 40 U DNaseI (Roche) for 30min at 37°C and subsequently purified by phenol-chloroform extraction and ethanol precipitation. rRNA was depleted using NEBNext rRNA depletion kit v2 (Human/Mouse/Rat) (NEB) and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions, starting with 600 ng total RNA input.

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

characteristic: INSDC center name

text: public

text: E-MTAB-12782_2:RNA_HEK_DIDO_KO.exon4_br1

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12782_2:RNA_HEK_DIDO_KO.exon4_br2

characteristic: Submitter Id

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_DIDO_KO.exon4_br3

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-dSPOC_br1

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-dSPOC_br2

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-dSPOC_br3

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO.exon4_br1

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO.exon4_br2

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO.exon4_br3

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO2_br1

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


text: BIMSB

text: public

characteristic: SRA accession

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO2_br2

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

characteristic: description

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_dSPOC-KO2_br3

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-dSPOC_br1

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-dSPOC_br2

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

characteristic: SRA accession

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-dSPOC_br3

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-KO.exon4_br1

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: description

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-KO.exon4_br2

text: ArrayExpress

text: not collected

text: human

text: Protocols: Cells from a 90% confluent 10 cm dish were harvested and counted, 8 million cells were mixed with 2 million Drosophila S2 cells as a spike-in control. Cell pellets from one well on a 6-well plate were resuspended in 1 mL TRI reagent (Sigma) and incubated for 5 min at room temperature. 200 µL chloroform (Applichem) was added and the lysate was vortexed and centrifuged at max. speed (21130g) for 15 min at 4°C. The aqueous layer was transferred to a new tube and precipitated with 0.5 mL isopropanol. The RNA pellet was isolated by centrifugation for 30 min at 4°C, washed with 1 mL 75% ethanol, re-centrifuged for 10 min, dried and resuspended in 70 µL RNase free water. 20 µg RNA was treated with 40 U DNaseI (Roche) for 30min at 37°C and subsequently purified by phenol-chloroform extraction and ethanol precipitation. rRNA was depleted using NEBNext rRNA depletion kit v2 (Human/Mouse/Rat) (NEB) and libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions, starting with 600 ng total RNA input.

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-12782_2:RNA_HEK_PHF3-DIDO_KO-KO.exon4_br3

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens

characteristic: title


text: BIMSB

text: public

characteristic: SRA accession

text: E-MTAB-12782_2:RNA_HEK_PHF3_d1595.2039_br1

characteristic: Submitter Id

text: ArrayExpress

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: embryo

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3_d1595.2039_br2

text: ArrayExpress

characteristic: broker name

text: not collected

text: human

characteristic: description

text: embryo

characteristic: developmental stage

characteristic: genotype

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BIMSB

text: public

text: E-MTAB-12782_2:RNA_HEK_PHF3_d1595.2039_br3

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: BIMSB

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: not collected

text: human

text: embryo

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: MCD, UMR5077, CBI

text: public

characteristic: SRA accession

tag: Namespace:MCD, UMR5077, CBI

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: not collected

characteristic: collection date

text: human

characteristic: common name

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. The 4C-seq experiments were realized as in Matelot and Noordermeer (2016) with minor modifications. Briefly, 15 million DIvA cells were cross-linked with 2% formaldehyde for 10 min at RT and the reaction was stopped using glycine (0,125M final) for 5min on ice. Cells were lysed, permeabilized with A50µL SDS 0,5% and digested with MboI (New England Biolabs). Three rounds of 4 h of digestion with MboI were necessary. Digested DNA was then ligated with a T4 DNA ligase (HC) (Promega), purified and digested with NlaIII overnight (New England Biolabs). After a second ligation step, DNA was purified before proceeding to the library preparation. For DNA purification steps, AMPure XP beads (Beckman Coulter) were used diluted at 1:10 in 20% PEG solution (PEG 8000 (Sigma) 20%, 2.5M NaCl, Tween 20 20%, Tris pH8 10mM, EDTA 1mM). For 4C-seq library preparation, 800ng-900ng of 4C-seq template was amplified using 16 individual PCR reactions with inverse primers (PAGE-purified) including the Illumina adapter sequences and a unique index for each condition. Libraries were purified with the QIAquick PCR Purification Kit (Qiagen). The primer sequences used to amplify each viewpoint were: Ctrl: FW:ATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTCAGGTTATCATCCCAA REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACCTTCGCTGTACCTTTG DSB1: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAACCTGGCAACTTATGAATCAGGA REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTATGTCAAAAGCCAAGGGGACA DSB2: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTTACGATTATTTGTGAATTTTG REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCTAATTCTGAGTTACATACATT DSB3: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGATTACGTAGAAGGGTGCC REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGGCAAATGATAACCCTGT DSB4: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGGTTATACTAAGATGTCAGTTCCT REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACGCACCTGGTTTAGATT

text: osteosarcoma

characteristic: disease

text: AsiSI-ER

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siARP2_mOHT

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. Cells were then lysed in cytoplasmic lysis buffer (50mM HEPES pH7.9, 10mM KCl2, 1.5mM MgCl2, 0.34M sucrose, 0.5% triton X-100, 10% glycerol, 1mM DTT) for 10 minutes on ice, then washed once in cytoplasmic lysis buffer before lysis in genomic extraction buffer (50mM Tris pH8.0, 5mM EDTA, 1% SDS, 0.5mg/mL proteinase K). Lysate was incubated at 60°C for 1 h. Genomic DNA was then ethanol precipitated on ice for 1h, pelleted at 19,000g for 20 min and washed twice in 75% ethanol. Genomic DNA was then used in a multiplex PCR reaction that amplified 25 target sites; 20 AsiSI cut sites and 5 uncut control sites. Amplicons were size selected using SPRIselect beads (Beckman, B23318) and subjected to DNA library preparation via the NEBNext Ultra II kit (NEB, E7645L).

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siCtrl_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


text: MCD, UMR5077, CBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_A_siSCC1_mOHT

characteristic: Submitter Id

text: ArrayExpress

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siSUN2_mOHT

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_B_siARP2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: E-MTAB-10865_3:Amplicon-seq_B_siCtrl_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

text: public

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_B_siSCC1_mOHT

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_B_siSUN2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siARP2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_C_siCtrl_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siSCC1_mOHT

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siSUN2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siARP2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_D_siCtrl_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siSCC1_mOHT

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siSUN2_mOHT

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. Hi-C experiments were performed in DIvA cells using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 1 million cells were used by condition. Briefly, cells were cross-linked with 2% formaldehyde for 10 min at RT, lysed and chromatin was digested with two different restriction enzymes included in the kit. Ends were filled-in in the presence of biotinylated nucleotides, followed by subsequent ligation. Ligated DNA was sonicated using the Covaris S220 to an average fragment size of 350 bp with the following parameters (Peak incident power: 140; Duty factor: 10%; Cycles per burst: 200; Treatment time: 70s). DNA was then subjected to a double-size selection to retain DNA fragments between 200 and 600 bp using Ampure XP beads (Beckman Coulter). Biotin-ligated DNA was precipitated with streptavidin-coupled magnetic beads (included in the kit). Hi-C library was prepared on beads using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) following instructions from the Arima Hi-C kit.

characteristic: description

text: osteosarcoma

text: AsiSI-ER

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Hi-C

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. qDRIP-seq was adapted from Crossley et al, NAR, 2020. In brief, 2.5 × 10 6 of trypsinized DIvA cells were mixed to 1.67 × 10 6 Drosophila S2 cells and lysed overnight at 37°C in TE buffer containing 0.5% SDS and 800 μg proteinase K (Roche, 03115828001). DNA was extracted by phenol:chloroform extraction using phase lock tubes (Qiagen, MaxTract, 129065) followed by ethanol precipitation. DNA was resuspended on ice in 130 μl TE buffer before sonication in Covaris S220 (microtubes PN520045) to obtain ~300 bp DNA fragments (Covaris S220, 140W peak incident power, 10% Duty factor, 200 cycles per burst for 80 sec). Immunoprecipitation was performed in triplicate by incubating 4 μg of sonicated DNA with 10 μg of S9.6 antibody (Antibodies Incorporation) in 1x binding buffer (10 mM NaPO 4 , 140 mM NaCl, 0.05 % Triton X100) overnight and at 4°C. Agarose A/G beads (Thermo Scientific, 20421) we added to samples for 2 h at 4°C. Beads were washed 4 times in binding buffer followed by incubation with elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, 0.3 μg/μL proteinase K) for 45 min at 55°C. Samples were subjected to phenol:chloroform extraction and ethanol precipitation, and were resuspended in low EDTA TE. Sequencing libraries were prepared using the Swift ACELL-NGS 1S Plus kit according to the manufacturer’s instructions using 12 PCR cycles. Libraries were pooled at equimolar concentrations.

text: osteosarcoma

text: AsiSI-ER

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: qDRIP-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. RNA-seq library preparation were performed at EMBL Genomics core facilities (Heidelberg, Germany) using TruSeq Stranded Total RNA (Illumina).

text: osteosarcoma

text: AsiSI-ER

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: RNA-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. The 4C-seq experiments were realized as in Matelot and Noordermeer (2016) with minor modifications. Briefly, 15 million DIvA cells were cross-linked with 2% formaldehyde for 10 min at RT and the reaction was stopped using glycine (0,125M final) for 5min on ice. Cells were lysed, permeabilized with A50µL SDS 0,5% and digested with MboI (New England Biolabs). Three rounds of 4 h of digestion with MboI were necessary. Digested DNA was then ligated with a T4 DNA ligase (HC) (Promega), purified and digested with NlaIII overnight (New England Biolabs). After a second ligation step, DNA was purified before proceeding to the library preparation. For DNA purification steps, AMPure XP beads (Beckman Coulter) were used diluted at 1:10 in 20% PEG solution (PEG 8000 (Sigma) 20%, 2.5M NaCl, Tween 20 20%, Tris pH8 10mM, EDTA 1mM). For 4C-seq library preparation, 800ng-900ng of 4C-seq template was amplified using 16 individual PCR reactions with inverse primers (PAGE-purified) including the Illumina adapter sequences and a unique index for each condition. Libraries were purified with the QIAquick PCR Purification Kit (Qiagen). The primer sequences used to amplify each viewpoint were: Ctrl: FW:ATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTCAGGTTATCATCCCAA REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACCTTCGCTGTACCTTTG DSB1: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTAACCTGGCAACTTATGAATCAGGA REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTATGTCAAAAGCCAAGGGGACA DSB2: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCTTACGATTATTTGTGAATTTTG REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGCTAATTCTGAGTTACATACATT DSB3: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGATTACGTAGAAGGGTGCC REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTAAGGCAAATGATAACCCTGT DSB4: FW:AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGGTTATACTAAGATGTCAGTTCCT REV:CAAGCAGAAGACGGCATACGAGAT(index6bp)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCACGCACCTGGTTTAGATT

text: osteosarcoma

characteristic: disease

text: AsiSI-ER

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siARP2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. Cells were then lysed in cytoplasmic lysis buffer (50mM HEPES pH7.9, 10mM KCl2, 1.5mM MgCl2, 0.34M sucrose, 0.5% triton X-100, 10% glycerol, 1mM DTT) for 10 minutes on ice, then washed once in cytoplasmic lysis buffer before lysis in genomic extraction buffer (50mM Tris pH8.0, 5mM EDTA, 1% SDS, 0.5mg/mL proteinase K). Lysate was incubated at 60°C for 1 h. Genomic DNA was then ethanol precipitated on ice for 1h, pelleted at 19,000g for 20 min and washed twice in 75% ethanol. Genomic DNA was then used in a multiplex PCR reaction that amplified 25 target sites; 20 AsiSI cut sites and 5 uncut control sites. Amplicons were size selected using SPRIselect beads (Beckman, B23318) and subjected to DNA library preparation via the NEBNext Ultra II kit (NEB, E7645L).

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_A_siCtrl_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siSCC1_pOHTpIAA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_A_siSUN2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_B_siARP2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_B_siCtrl_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_B_siSCC1_pOHTpIAA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_B_siSUN2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siARP2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_C_siCtrl_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siSCC1_pOHTpIAA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_C_siSUN2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siARP2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: description

text: osteosarcoma

text: AsiSI-ER-AID

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10865_3:Amplicon-seq_D_siCtrl_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siSCC1_pOHTpIAA

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: osteosarcoma

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: Amplicon-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

text: E-MTAB-10865_3:Amplicon-seq_D_siSUN2_pOHTpIAA

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

characteristic: common name

text: osteosarcoma

characteristic: disease

text: AsiSI-ER-AID

text: not collected

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: Amplicon-seq

characteristic: protocol

text: Homo sapiens

characteristic: title


characteristic: ENA-CHECKLIST

text: MCD, UMR5077, CBI

characteristic: INSDC first public

text: public

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. Hi-C experiments were performed in DIvA cells using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 1 million cells were used by condition. Briefly, cells were cross-linked with 2% formaldehyde for 10 min at RT, lysed and chromatin was digested with two different restriction enzymes included in the kit. Ends were filled-in in the presence of biotinylated nucleotides, followed by subsequent ligation. Ligated DNA was sonicated using the Covaris S220 to an average fragment size of 350 bp with the following parameters (Peak incident power: 140; Duty factor: 10%; Cycles per burst: 200; Treatment time: 70s). DNA was then subjected to a double-size selection to retain DNA fragments between 200 and 600 bp using Ampure XP beads (Beckman Coulter). Biotin-ligated DNA was precipitated with streptavidin-coupled magnetic beads (included in the kit). Hi-C library was prepared on beads using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina and NEBNext® Multiplex Oligos for Illumina (New England Biolabs) following instructions from the Arima Hi-C kit.

characteristic: description

text: osteosarcoma

text: AsiSI-ER

characteristic: genotype

text: not collected

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: bone

characteristic: organism part

text: Hi-C

text: Homo sapiens


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: MCD, UMR5077, CBI

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: epithelial cell

text: not collected

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. qDRIP-seq was adapted from Crossley et al, NAR, 2020. In brief, 2.5 × 10 6 of trypsinized DIvA cells were mixed to 1.67 × 10 6 Drosophila S2 cells and lysed overnight at 37°C in TE buffer containing 0.5% SDS and 800 μg proteinase K (Roche, 03115828001). DNA was extracted by phenol:chloroform extraction using phase lock tubes (Qiagen, MaxTract, 129065) followed by ethanol precipitation. DNA was resuspended on ice in 130 μl TE buffer before sonication in Covaris S220 (microtubes PN520045) to obtain ~300 bp DNA fragments (Covaris S220, 140W peak incident power, 10% Duty factor, 200 cycles per burst for 80 sec). Immunoprecipitation was performed in triplicate by incubating 4 μg of sonicated DNA with 10 μg of S9.6 antibody (Antibodies Incorporation) in 1x binding buffer (10 mM NaPO 4 , 140 mM NaCl, 0.05 % Triton X100) overnight and at 4°C. Agarose A/G beads (Thermo Scientific, 20421) we added to samples for 2 h at 4°C. Beads were washed 4 times in binding buffer followed by incubation with elution buffer (50 mM Tris pH 8, 10 mM EDTA, 0.5% SDS, 0.3 μg/μL proteinase K) for 45 min at 55°C. Samples were subjected to phenol:chloroform extraction and ethanol precipitation, and were resuspended in low EDTA TE. Sequencing libraries were prepared using the Swift ACELL-NGS 1S Plus kit according to the manufacturer’s instructions using 12 PCR cycles. Libraries were pooled at equimolar concentrations.

text: osteosarcoma

text: AsiSI-ER

text: not collected

characteristic: geographic location (country and/or sea)

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: bone

text: qDRIP-seq

text: Homo sapiens


characteristic: External Id

text: MCD, UMR5077, CBI

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: epithelial cell

text: not collected

characteristic: collection date

text: human

text: Protocols: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with antibiotics, 10% FCS (InVitrogenInvitrogen) with 1 µg/mL puromycin (DIvA cells) at 37°C under a humidified atmosphere with 5% CO2. For AsiSI-dependent DSB induction, cells were treated with 300 nM OHT (Sigma; H7904) for 4h or 24h. For ATM inhibition, cells were pretreated for 1 h with 20μM KU-55933 (Sigma, SML1109) and during subsequent 4OHT treatment. For DNA-PK inhibition, cells were pretreated for 1 h with 2μM NU-7441 (Selleckchem, S2638) and during subsequent 4OHT. siRNA transfection were performed using the 4D Nucleofector X (kit SE cell line) according to the manufacturer's instructions and subsequent treatment(s) were performed 48 h later. siRNA sequences: CTRL: CAUGUCAUGUGUCACAUCU; or SCC1: GGUGAAAAUGGCAUUACGG: or SMC1 (siSMC1): UAGGCUUCCUGGAGGUCACAUUUAA; or 53BP1 (si53BP1): GAACGAGGAGACGGUAAUA; or SUN2 (siSUN2): CGAGCCTATTCAGACGTTTCA; or ARP2 (siARP2): GGCACCGGGUUUGUGAAGU or SETX (siSETX): GAGAGAAUUAUUGCGUACU. For cell synchronization, cells were incubated for 18 h with 2 mM thymidine (Sigma, T1895), then released during 11 h, followed by a second thymidine treatment for 18 hr. S, G2 and G1 cells were then respectively treated with OHT at, 0, 6 or 11 h following thymidine release and harvested 4 h later. RNA-seq library preparation were performed at EMBL Genomics core facilities (Heidelberg, Germany) using TruSeq Stranded Total RNA (Illumina).

text: osteosarcoma

text: AsiSI-ER

text: not collected

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: bone

text: RNA-seq

text: Homo sapiens


characteristic: ENA-CHECKLIST

text: University of Copenhagen

characteristic: INSDC first public

text: public

tag: Namespace:University of Copenhagen

text: not provided

text: muskox

characteristic: common name

text: muskox

text: Russia

text: Wrangel Island

characteristic: geographic location (region and locality)

text: Ovibos moschatus

text: Ovibos moschatus

text: muskox

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: University of Salerno

text: public

tag: Namespace:University of Salerno

text: ArrayExpress

text: not collected

text: Protocols: 109 bacterial isolates were collected from four hospitals in the Campania region (Southern Italy).Bacterial isolation was performed via routine methods using mycobacterial growth indicator tubes (Bactec MGIT 960; Becton Dickinson, Sparks, MD, US) and Lowenstein-Jensen agar slants. Genomic DNA was obtained from clinical strains using two column-based DNA extraction methods (QIAamp DNA minikit, Qiagen, Germany), according to the instructions. The purified DNA was qualitatively and quantitatively evaluated using NanoDrop and Qubit dsDNA analysis kits (ThermoFisher Scientific, Waltham, MA, USA). Indexed libraries were prepared starting from 60 ng of each DNA sample according to Illumina DNA Prep sample preparation kits (Illumina Inc., San Diego, CA, USA). Final libraries concentrations and size were assessed with Quant-IT DNA Assay Kit and Agilent 4200 Tapestation System (Agilent Technologies, Milan, Italy), respectively.

characteristic: description

text: not collected

text: not applicable

characteristic: isolate

characteristic: lineage

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: strain


characteristic: ENA-LAST-UPDATE

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

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

text: COVID-19 Genomics UK Consortium

characteristic: collecting institution

text: not provided

characteristic: collector name

text: not provided

characteristic: definition for seropositive sample

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: England

text: not provided

characteristic: host common name

text: not provided

characteristic: host health state

text: Human

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: not provided

characteristic: serotype (required for a seropositive sample)

text: not provided

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

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

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: COVID-19 Genomics UK Consortium

characteristic: broker name

characteristic: collection date

text: not provided

text: not provided

text: United Kingdom

text: England

characteristic: geographic location (region and locality)

text: not provided

text: not provided

text: Human

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: not provided

characteristic: title

text: not provided


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: Department of Clinical Microbiology, Slagelse Sygehus

characteristic: collecting institution

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

characteristic: host common name

characteristic: host description

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

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Department of Clinical Microbiology, Esbjerg Sygehus

characteristic: collecting institution

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2022-01-31

characteristic: host description

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-41150/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2022-03-14

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Department of Clinical Microbiology, Herlev and Gentofte University Hospital

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2022-02-14

characteristic: host description

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2022-01-10

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

characteristic: host description

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2022-02-07

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2022-01-03

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_date=2022-03-07

characteristic: host description

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2022-12-19

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2021-12-13

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

characteristic: host description

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: active surveillance in response to outbreak


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-653482/2022

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-12671/2020

characteristic: host description

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2022-06-20

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=3,last_infection_date=2022-01-17

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-305252/2021

characteristic: host description

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Department of Clinical Microbiology, Herlev and Gentofte University Hospital

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2021-08-09

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=3,last_infection_date=2022-11-07

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-461892/2022

characteristic: host description

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2022-02-07

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

characteristic: host description

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-322295/2022

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-71893/2021

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

characteristic: host description

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

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_date=2022-01-17

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

text: Severe acute respiratory syndrome coronavirus 2

characteristic: sample capture status


characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2022-02-14

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

text: active surveillance in response to outbreak

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Statens Serum Institut and the Danish Covid19 Genome Consortium (DCGC)

text: public

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

text: Human

characteristic: host common name

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-301486/2022

characteristic: host description

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: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collecting institution

characteristic: collection date

text: Danish Covid-19 Genome Consortium

text: Original

text: Denmark

characteristic: geographic location (region and locality)

text: Human

text: n_infections=2,last_infection_id=hCoV-19/Denmark/DCGC-521271/2022

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: Danish Covid-19 Genome Consortium

characteristic: collector name

text: Original

characteristic: description

text: Denmark

characteristic: geographic location (country and/or sea)

text: Human

text: n_infections=2,last_infection_date=2022-03-28

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: isolate

characteristic: organism

characteristic: title