characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score poor

characteristic: clinical information

text: sorafenib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


status: PUBLIC

tag: attribute

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:General medical oncology, University Hospitals Leuven

characteristic: Submitter Id

unit: year

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

text: Protocols: We selected primary ccRCC samples from the Leuven University Hospitals ccRCC tumor bank, which prospectively collects tissue and detailed clinical data from metastatic ccRCC patients after informed consent. Patients were eligible if archived tissue of the primary tumor was available, provided they had not received systemic therapy prior to tissue retrieval. Clear-cell histology was confirmed by an expert uro-pathologist. As a reference, we included paired normal kidney samples from 16 patients as well (healthy tissue block from the nephrectomy specimen removed during ccRCC surgery). H&E-stained sections of the tumor sample were examined by a pathologist to confirm the diagnosis and to estimate tumor content. In the discovery series, tumor content was above 90% in 71 cases and was 70% in 3 cases. Formallin-fixed paraffin-embedded samples were trimmend and dissected in 10µl sections, of which 4-6 whole 10-μm sections were used for RNA extraction. Batch 2014: RNA samples were extracted with the \RecoverAll Total Nucleic Acid Isolation Kit for FFPE\ (Ambion). Sample RNA Integrity Numbers were in the range 1.7 to 2.5 when assayed on an Agilent 2100 Bioanalyzer. Batch 2017: RNA samples were extracted with the \RecoverAll Total Nucleic Acid Isolation Kit for FFPE\ (Ambion). Sample RNA Integrity Numbers were less than 3 when assayed on an Agilent 2100 Bioanalyzer Batch 2014: Sample amounts used ranged between 200 and 500ng of total RNA. They were processed with kit \NEBNext Multiplex Small RNA Library Prep Set for Illumina\ (NEB part # E7300 v2.1) by following manufacturer instructions. Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with ProtoScript II Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by PCR with LongAmp Taq DNA polymerase mix (12 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 140 to 150 bases -expected to include both miRNA and piRNA libraries- was extracted. Batch 2017: 1000ng of total RNA per sample was processed with kit \NEBNext Multiplex Small RNA Library Prep Set for Illumina\ (NEB E7300) by following manufacturer instructions. Briefly, samples were sequentially ligated to 3' and 5' adapters, with the truncated form of T4 RNA Ligase 2 and the T4 RNA ligase 1, respectively. Reverse transcription with ProtoScript II Reverse Transcriptase yielded cDNA adapter-ligated libraries that were amplified by PCR with LongAmp Taq DNA polymerase mix (15 cycles). Amplified barcoded cDNA from different samples was pooled, and a polyacrylamide gel electrophoresis fraction of 140 to 150 bases -expected to include both miRNA and piRNA libraries- was extracted.

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

unit: month

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

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text: General medical oncology, University Hospitals Leuven

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

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characteristic: INSDC status

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text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: pazopanib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

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text: public

characteristic: age

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text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: no or censored

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

text: not reached

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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text: ArrayExpress

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text: adult

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text: clear cell renal carcinoma

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text: yes

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text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

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text: FFPE specimen

characteristic: title


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text: public

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text: yes

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text: ArrayExpress

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text: IMDC risk score poor

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text: sunitinib

characteristic: clinical treatment

text: human

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text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

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text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

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text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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text: yes

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text: sunitinib

text: human

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text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

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text: yes

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text: Homo sapiens

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text: Homo sapiens

text: kidney

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text: yes

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text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

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text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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text: yes

text: ArrayExpress

text: IMDC risk score poor

text: sunitinib

text: human

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characteristic: developmental stage

text: clear cell renal carcinoma

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text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

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characteristic: ENA-CHECKLIST

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text: yes

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characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

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text: sunitinib

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text: adult

text: clear cell renal carcinoma

text: no or censored

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

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characteristic: ENA-CHECKLIST

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text: public

characteristic: age

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text: yes

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text: ArrayExpress

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characteristic: ccRCC transcriptomic subtype

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text: yes

characteristic: disease progression at data cutoff

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text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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text: public

characteristic: INSDC status

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text: ArrayExpress

text: IMDC risk score good

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score poor

characteristic: clinical information

text: pazopanib

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characteristic: common name

text: adult

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text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: no or censored

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: no or censored

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sorafenib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: no or censored

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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characteristic: External Id

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text: yes

text: ArrayExpress

text: IMDC risk score poor

text: sorafenib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

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text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

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text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score poor

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

text: pazopanib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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characteristic: INSDC center name

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: no or censored

text: ArrayExpress

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score good

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: no or censored

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: age

characteristic: age at diagnosis

text: no or censored

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score poor

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: no or censored

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: yes

text: ArrayExpress

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score poor

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title

text: not available


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score intermediate

characteristic: clinical information

text: pazopanib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score good

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: no or censored

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score poor

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score good

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: pazopanib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score poor

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: no or censored

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

text: IMDC risk score intermediate

characteristic: clinical information

text: sorafenib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score poor

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

text: not reached

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score poor

text: pazopanib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: no or censored

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: no or censored

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sorafenib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score good

characteristic: clinical information

text: pazopanib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sorafenib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

text: neoplasm

text: Homo sapiens

text: female

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: public

characteristic: age

characteristic: age at diagnosis

text: no or censored

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score intermediate

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: male

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

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

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: pazopanib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

characteristic: age

characteristic: age at diagnosis

text: yes

characteristic: alive at endpoint

text: ArrayExpress

characteristic: broker name

characteristic: ccRCC transcriptomic subtype

text: IMDC risk score good

characteristic: clinical information

text: sunitinib

characteristic: clinical treatment

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: yes

characteristic: disease progression at data cutoff

characteristic: mirnaseq date

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: progression free survival

text: neoplasm

characteristic: sampling site

text: Homo sapiens

text: female

text: FFPE specimen

characteristic: specimen with known storage state

characteristic: survival time

characteristic: tumor shrinkage (according to recist v1.1)


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: yes

text: ArrayExpress

text: IMDC risk score intermediate

text: sunitinib

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: yes

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

characteristic: organism part

characteristic: related experiment E-MTAB-10592 source name

text: neoplasm

text: Homo sapiens

text: male

characteristic: sex

text: FFPE specimen

characteristic: title


E-MTAB-10642:Sample 1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wageningen University & Research

text: public

text: E-MTAB-10642:Sample 1

tag: Namespace:Wageningen University & Research

unit: hour

characteristic: age

text: ArrayExpress

characteristic: broker name

text: Protocols: Samples were collected by washing the animals off the NGM plate using M9 buffer. After collection by centrifugation and removing the supernatant, pellets were immediately flash-frozen in liquid nitrogen. For the single-sex experiments male and hermaphrodite nematodes were separated ~44 hours post bleaching by placing them on fresh plates. After 200 nematodes were handpicked per plate the populations were washed into an Eppendorf tube and infected 48 hours post bleaching as described previously (Sterken et al., 2014). Mock infections were performed by adding M9 instead of OrV unless indicated that a mock lysate (lysate of uninfected nematodes) was used. The experiment was performed in technical duplicate, therefore every sample contained ~400 nematodes. The samples for small RNA (sRNA) sequencing contained ~600 nematodes. However, for some experiments, not enough males (less than 400) were present on the plates to pick males from and in these cases a total of 200 male nematodes were picked per sample (and also for the hermaphrodite samples within the same experimental batch). Infected populations were collected 30 hours post infection (78 hours post bleaching). Viral loads were obtained as described by (Sterken et al., 2014). RNA isolation was performed using the Maxwell® 16 AS2000 instrument with the Maxwell® 16 LEV simply RNA Tissue Kit (Promega). The recommended protocol was followed, except for adding 10mg of proteinase K per sample after addition of the lysis buffer. The lysis was performed in a shaker for 10 minutes at 65ºC (1000rpm) (Eppendorf). RNA sample quantity and quality were measured by using NanoDrop (Thermo Scientific). Libraries were constructed by BGI. The RNA was size-fractioned (18-30nt), and 5' and 3' adapters were ligated. Thereafter cDNA was generated using Reverse transcription and the sequences were amplified by PCR.

text: adult

text: wild type genotype

characteristic: genotype

text: Orsay virus

characteristic: infect

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: male

characteristic: strain

text: Sample 1


E-MTAB-10642:Sample 2

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10642:Sample 2

characteristic: Submitter Id

text: ArrayExpress

characteristic: description

text: adult

text: wild type genotype

text: Orsay virus

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

text: Sample 2


E-MTAB-10642:Sample 3

text: Wageningen University & Research

text: public

text: E-MTAB-10642:Sample 3

text: ArrayExpress

text: adult

characteristic: developmental stage

text: wild type genotype

text: Caenorhabditis elegans

characteristic: organism

text: Caenorhabditis elegans

text: whole organism

characteristic: organism part

text: Caenorhabditis elegans

text: male

characteristic: sex

text: Sample 3

characteristic: title


E-MTAB-10642:Sample 4

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wageningen University & Research

text: public

text: E-MTAB-10642:Sample 4

characteristic: age

text: ArrayExpress

characteristic: broker name

text: adult

text: wild type genotype

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

text: Sample 4


E-MTAB-10642:Sample 5

characteristic: External Id

text: Wageningen University & Research

characteristic: INSDC center name

text: public

text: E-MTAB-10642:Sample 5

text: ArrayExpress

text: adult

text: wild type genotype

characteristic: genotype

text: Orsay virus

characteristic: infect

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: male

characteristic: strain

text: Sample 5


E-MTAB-10642:Sample 6

text: Wageningen University & Research

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10642:Sample 6

characteristic: Submitter Id

text: ArrayExpress

text: adult

text: wild type genotype

text: Orsay virus

text: Caenorhabditis elegans

text: Caenorhabditis elegans

text: whole organism

text: Caenorhabditis elegans

text: hermaphrodite

text: Sample 6


text: Robert Koch Institute

text: public

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10334-CVDP-153CA130-E62C-4C25-9937-83455F900692

tag: Namespace:Robert Koch Institute

text: RKI-OSEDA

text: Carl-Thiem-Klinikum Cottbus - Zentrum für Laboratoriumsmedizin Mikrobiologie und Krankenhaushygiene, Thiemstr. 111; 03048 Cottbus

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Brandenburg

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

text: active surveillance in response to outbreak

characteristic: sample capture status

text: Molecular surveillance of SARS-CoV-2 in Germany


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

text: IMS-10334-CVDP-073B6815-3BA9-4E1F-9C48-FA5BE12365F6

text: RKI-OSEDA

characteristic: broker name

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


text: Robert Koch Institute

text: public

characteristic: SRA accession

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10334-CVDP-436996E8-381B-44B3-87EF-4FA200D051DF

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: collecting institution

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Brandenburg

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

text: public

text: Random sampling

text: IMS-10334-CVDP-DCB99BBB-FE1F-43FD-BF6D-4435E42E2A83

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: sample capture status


text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Random sampling

characteristic: Sampling Strategy

text: IMS-10334-CVDP-F1E755E1-543D-40F3-BECA-CFD4BDCF3814

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

characteristic: collecting institution

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

text: public

text: Suspect sampling

text: IMS-10334-CVDP-C5F266BB-4D2F-4C36-B912-B4B42FD57CBB

text: RKI-OSEDA

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Brandenburg

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: not provided

text: not provided


text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Random sampling

text: IMS-10334-CVDP-91EDEA13-9C49-4AB8-AFF8-563C04CC04EA

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: sample capture status


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

text: public

characteristic: SRA accession

text: Suspect sampling

characteristic: Sampling Strategy

text: IMS-10334-CVDP-DFC78233-2D61-48C6-A77B-345340B97A87

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

characteristic: collecting institution

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Suspect sampling

text: IMS-10334-CVDP-F87DC848-499E-46AF-BFB5-1F9FEAEAD895

text: RKI-OSEDA

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Brandenburg

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: not provided

text: not provided


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

text: public

text: Random sampling

text: IMS-10334-CVDP-4AC35564-431C-4FF7-9438-6ADC27A06E71

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

characteristic: host subject id

text: not provided

characteristic: isolate

characteristic: organism

characteristic: sample capture status


text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Suspect sampling

characteristic: Sampling Strategy

text: IMS-10334-CVDP-5070AB15-AEDA-44DB-8664-9C3DD9169B1F

characteristic: Submitter Id

text: RKI-OSEDA

characteristic: broker name

characteristic: collecting institution

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

text: not provided

text: not provided

text: not provided

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Robert Koch Institute

text: public

text: Random sampling

text: IMS-10334-CVDP-24BBF74E-29F0-4657-9397-0BE9CD379FAB

text: RKI-OSEDA

characteristic: collection date

text: not provided

characteristic: collector name

text: Germany

characteristic: geographic location (country and/or sea)

text: Europe/Germany/Brandenburg

characteristic: geographic location (region and locality)

text: Human

characteristic: host common name

text: not provided

characteristic: host health state

text: Homo sapiens

text: not provided

text: not provided

text: not provided


text: Robert Koch Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Suspect sampling

text: IMS-10334-CVDP-D4A09E8F-79FE-46AE-8EF3-7D0D267ACEF7

text: RKI-OSEDA

text: not provided

text: Germany

text: Europe/Germany/Brandenburg

text: Human

text: not provided

text: Homo sapiens

characteristic: host scientific name

text: not provided

characteristic: host sex

text: not provided

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characteristic: collection date

text: not provided

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characteristic: geographic location (region and locality)

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