characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_noEIF4E2_g2_1_NA_ribo6

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 6

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


status: PUBLIC

tag: attribute

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_noEIF4E2_g2_1_NA_ribo7

tag: Namespace:The Francis Crick Institute

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 7

characteristic: fraction

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_noEIF4E2_g2_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo1

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo2

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo5

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo4

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g1_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_noEIF4E2_g2_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_2_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: empty vector

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: empty vector

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_noVHL_EIF4E2_NA_4_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: empty vector

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo2

text: ArrayExpress

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_2_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo3

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 3

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo2

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 2

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: renal cell adenocarcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_786O_VHL_EIF4E2_NA_4_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: renal cell adenocarcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo3

text: ArrayExpress

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_1_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_NA_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo6

text: ArrayExpress

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_3_Torin1_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_noVHL_EIF4E2_NA_4_Torin1_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo2

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 2

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo3

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 3

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo6

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 6

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo5

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 5

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo7

text: ArrayExpress

text: human

text: Protocols: The VHL-defective kidney cancer cell lines, RCC4 and 786-O, were used. These cell lines were modified either by lentiviral transduction (to re-introduce VHL or an empty vector as control) and/or by CRISPR/Cas9-mediated genome editing of the EIF4E2 locus. Cells were grown on 15 cm dishes in DMEM with 1 mM sodium pyruvate, 10% FBS and 5 µg/mL blasticidin at 37 ˚C in 5% CO2. mTOR activity was inhibited by treating the cells with 250 nM of Torin 1 for 2 hours. mRNA translation was arrested by treating the cells with 100 µg/mL cycloheximide for 3 min prior to harvesting the cells. Cells were washed with ice-cold PBS with 100 µg/mL cycloheximide, and lysed using cytoplasmic lysis buffer. The cytoplasmic lysate was fractionated according to the number of associated ribosomes using sucrose density gradients and ultracentrifugation. RNA from the polysome fractionated samples was extracted using an RNA clean and concentrator-5 kit (Zymo Research, R1016) according to the manufacturer’s instructions, with the following modifications: 322.5 µL of preconditioned RNA binding buffer (157.5 µL of RNA binding buffer (supplied with RNA clean and concentrator-5 kit), 157.5 µL of absolute EtOH and 7.5 µL of 20% SDS) was added to 150 µL of the fractionated samples before loading to the column. 5′ end-Seq was performed on the extracted total RNA. In short, a full-length cDNA library was generated using a combined reverse transcription and template switching reaction, followed by PCR amplification. The amplified libraries were multiplexed, and then purified using ProNex beads (Promega). The 3′ end of the cDNA library (i.e. 5′ end of mRNAs) was amplified specifically using Tn5 transposase-mediated tagmentation and PCR amplification with primers annealing to the appropriate adapters added by the template switching reaction and tagmentation. The PCR primers contained i5 and i7 Illumina index sequences and the amplified libraries were multiplexed.

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_3_Torin1_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo1

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 1

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo3

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 3

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo2

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 2

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo4

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 4

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo5

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: common name

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 5

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: The Francis Crick Institute

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo6

text: ArrayExpress

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: clear cell renal carcinoma

characteristic: disease

text: ribopolysome fraction 6

characteristic: fraction

text: VHL lentivirus

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

text: Homo sapiens


text: The Francis Crick Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo7

text: ArrayExpress

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 7

text: VHL lentivirus

characteristic: genotype

text: not applicable

text: Homo sapiens

text: Homo sapiens

text: kidney

characteristic: organism part

text: Homo sapiens

characteristic: stimulus

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: The Francis Crick Institute

characteristic: INSDC last update

text: public

text: E-MTAB-10689:polysome_RCC4_VHL_EIF4E2_NA_4_Torin1_ribo8

text: ArrayExpress

characteristic: broker name

text: human

text: adult

text: clear cell renal carcinoma

text: ribopolysome fraction 8

text: VHL lentivirus

text: not applicable

characteristic: isolate

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: kidney

text: Homo sapiens