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characteristic: description

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characteristic: ENA-CHECKLIST

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tag: Namespace:Anthony Smith, NICD

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text: A. Smith, National Institute for Communicable Diseases

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text: Whole genome sequencing data uploaded by EnteroBase user

text: South Africa, Gauteng

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text: Vibrio cholerae

text: Vibrio cholerae

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text: Anthony Smith, NICD

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text: Zimbabwe, Manicaland

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text: Anthony Smith, NICD

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text: Zimbabwe, Mashonaland East

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text: Anthony Smith, NICD

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text: Anthony Smith, NICD

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text: EnteroBase

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text: South Africa, Western Cape

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text: Anthony Smith, NICD

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text: South Africa, Western Cape

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text: Anthony Smith, NICD

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text: Anthony Smith, NICD

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text: South Africa, Western Cape

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text: Salmonella enterica

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text: Anthony Smith, NICD

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text: South Africa, Western Cape

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text: Anthony Smith, NICD

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text: South Africa, KwaZulu-Natal

text: Human, Urine

text: Salmonella enterica

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characteristic: ENA-CHECKLIST

text: Anthony Smith, NICD

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text: EnteroBase

text: EnteroBase

text: South Africa, North West

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text: Anthony Smith, NICD

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characteristic: broker name

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text: South Africa, Gauteng

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text: Anthony Smith, NICD

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text: EnteroBase

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text: South Africa, Western Cape

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text: Human, Stool

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text: Anthony Smith, NICD

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text: South Africa, Western Cape

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text: Anthony Smith, NICD

text: public

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text: South Africa, KwaZulu-Natal

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text: public

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text: South Africa, Eastern Cape

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text: public

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text: South Africa, Gauteng

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text: Anthony Smith, NICD

text: public

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text: South Africa, Gauteng

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text: public

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characteristic: broker name

text: EnteroBase

text: South Africa, KwaZulu-Natal

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text: Anthony Smith, NICD

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text: EnteroBase

characteristic: collection date

text: South Africa, Western Cape

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text: Human, Stool

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text: Salmonella enterica

text: Typhimurium


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text: Anthony Smith, NICD

text: public

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text: EnteroBase

text: South Africa, Eastern Cape

text: Human, Blood culture

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text: Enteritidis

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text: Anthony Smith, NICD

text: public

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text: South Africa, Eastern Cape

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Dublin


text: Anthony Smith, NICD

characteristic: INSDC center name

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text: South Africa, North West

text: Human, Blood culture

text: Salmonella enterica

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text: Salmonella enterica

text: Enteritidis


text: Anthony Smith, NICD

characteristic: INSDC first public

text: public

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text: EnteroBase

text: South Africa, Western Cape

text: Human, Blood culture

text: Salmonella enterica

text: Salmonella enterica

text: Enteritidis

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text: Anthony Smith, NICD

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text: public

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text: EnteroBase

text: EnteroBase

text: South Africa, Eastern Cape

text: Human, Other

text: Salmonella enterica

text: Salmonella enterica

text: Isangi


text: IAI - Institut des Agents Infectieux

text: public

characteristic: SRA accession

tag: Namespace:IAI - Institut des Agents Infectieux

text: cultured strain

characteristic: description

text: France

characteristic: geographic location (country and/or sea)

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

characteristic: isolate

text: Bronchoalveolar lavage fluid

text: Staphylococcus aureus

text: Staphylococcus aureus


characteristic: ENA-CHECKLIST

text: public

tag: Namespace:Institute of Molecular Oncology, Center for Tumor Biology and Immunology (ZTI), Philipps-University Marburg

characteristic: Submitter Id

unit: year

characteristic: age

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

characteristic: common name

text: Protocols: For generating exon-wide mutant cell libraries, 5.4 x 108 HCT116Δin5/LSL or HCT116Δin5+7/LSL cells were transfected with 1.125 mg pX459_blast_In5LSL or pX459_blast_In7LSL, and 1.125 mg of the corresponding HR700 vector library using Lipofectamine 2000 according to the manufacturer’s protocol. Transfected cells were selected with 20 µg/ml blasticidin for 3 days and 1 µg/ml puromycin for 7 days. 1.2 x 108 cells were infected with AV-Cre. The human colorectal carcinoma cell line HCT116 was obtained from the American Tissue Collection Center (ATCC, CCL-247) and cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco, 41966-029) supplemented with 10% heat-inactivated fetal bovine serum (FBS, Sigma-Aldrich, S0615) and 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco, 15140122). To ensure unambigous genotype-phenotype correlations, the cell were haploidized prior to CRISPR-editing by introducing inactivating deletions of intronic splicing into one of the two TP53 alleles, leaving only one functional copy of TP53. The remaining TP53 allele was altered by inserting a LoxP-flanked transcriptional stop cassette (Lox-Stop-Lox, LSL) into intron 4, which allowed reversible silencing of TP53 expression. The LSL cassette was then specifically targeted with CRISPR/Cas9 to introduce a variety of different mutant p53 alleles. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, 74106) and reverse transcribed using the SuperScript VILO cDNA Synthesis Kit (Invitrogen, 11754250). For cDNA sequencing of mutant cell libraries, RNA was reverse transcribed and amplified in 5 reactions with 1 µg RNA template using SuperScript IV One-Step RT-PCR System with ezDNase (Invitrogen, 12595025). The amplified PCR products were pooled, providing an estimated variant coverage of 50-250x, purified and diluted 1:1000 for a second step of PCR, using exon-specific primers and Q5 High-Fidelity DNA Polymerase.

text: adult

characteristic: developmental stage

text: colorectal cancer

characteristic: disease

text: targeted mutation (Exon 5)

characteristic: genetic modification

text: TP53 Δ/LSL

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colorectum

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Institute of Molecular Oncology, Center for Tumor Biology and Immunology (ZTI), Philipps-University Marburg

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: adult

text: colorectal cancer

text: targeted mutation (Exon 5)

text: TP53 Δ/LSL

text: not applicable

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: colorectum

text: Homo sapiens

text: male

characteristic: title


characteristic: ENA-CHECKLIST

text: public

characteristic: Submitter Id

characteristic: age

text: ArrayExpress

characteristic: broker name

text: intestinal epithelial cell

text: human

characteristic: common name

characteristic: description

text: adult

text: colorectal cancer

text: targeted mutation (Exon 6)

text: TP53 Δ/LSL

text: not applicable

characteristic: isolate

text: Homo sapiens

text: Homo sapiens

text: colorectum

text: Homo sapiens

text: male


characteristic: ENA-FIRST-PUBLIC

text: public

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: adult

characteristic: developmental stage

text: colorectal cancer

characteristic: disease

text: targeted mutation (Exon 7)

characteristic: genetic modification

text: TP53 Δ/LSL

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colorectum

characteristic: organism part

text: Homo sapiens

text: male

characteristic: sex


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

text: ArrayExpress

text: intestinal epithelial cell

text: human

text: adult

text: colorectal cancer

text: targeted mutation (Exon 8)

text: TP53 Δ/LSL

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: colorectum

text: Homo sapiens

text: male


characteristic: ENA-CHECKLIST

text: NVRL

text: public

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

text: hCov-19 Oxford Nanopore MinION reads obtained following the Artic v3 protocol

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Dublin

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

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characteristic: ENA-CHECKLIST

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characteristic: External Id

text: NVRL

characteristic: INSDC center name

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text: public

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characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Mayo

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/MO-NVRL-SIRL00017919/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Roscommon

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

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text: hCoV-19/Ireland/RN-NVRL-SIRL00017114/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Meath

text: human

text: not provided

text: not provided

text: Homo sapiens

text: male

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/MH-NVRL-SIRL00017119/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Dublin

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

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text: hCoV-19/Ireland/D-NVRL-SIRL00017024/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Westmeath

text: human

text: not provided

text: not provided

text: Homo sapiens

text: male

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/WH-NVRL-SIRL00017082/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Dublin

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

characteristic: sample capture status

text: hCoV-19/Ireland/D-NVRL-SIRL00017087/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Dublin

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/D-NVRL-SIRL00017117/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Carlow

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

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text: hCoV-19/Ireland/CW-NVRL-SIRL00017173/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: External Id

text: NVRL

characteristic: INSDC center name

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text: public

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text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

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text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Kildare

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/KE-NVRL-SIRL00017157/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Clare

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

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text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

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text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

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text: hCoV-19/Ireland/CE-NVRL-SIRL00017174/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

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characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Dublin

text: human

text: not provided

text: not provided

text: Homo sapiens

text: female

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/D-NVRL-SIRL00017049/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Galway

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: female

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

characteristic: sample capture status

text: hCoV-19/Ireland/G-NVRL-SIRL00017130/2023

characteristic: title

characteristic: virus identifier


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NVRL

characteristic: INSDC center name

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characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Irish Consortium for Sequencing Covid

characteristic: broker name

text: National Virus Reference Laboratory

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Human coronavirus 2019

characteristic: common name

characteristic: description

text: Ireland

text: Europe / Ireland / Dublin

text: human

text: not provided

text: not provided

text: Homo sapiens

text: male

text: not provided

text: Oro-Nasopharyngeal swab

text: hCoV-19/Ireland/D-NVRL-SIRL00017125/2023


text: NVRL

text: public

text: Irish Consortium for Sequencing Covid

text: National Virus Reference Laboratory

text: not provided

text: Human coronavirus 2019

text: Ireland

characteristic: geographic location (country and/or sea)

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: Europe / Ireland / Laois

characteristic: geographic location (region and locality)

characteristic: host age

text: human

characteristic: host common name

text: not provided

characteristic: host disease outcome

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

text: not provided

characteristic: host subject id

text: Oro-Nasopharyngeal swab

characteristic: isolation source host-associated

characteristic: organism

characteristic: sample capture status

text: hCoV-19/Ireland/LS-NVRL-SIRL00017144/2023

characteristic: title

characteristic: virus identifier