ERX1228389 E-MTAB-4091:siGlo_Poly1 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989642 SAMEA3682493 E-MTAB-4091:siGlo_Poly1 siGlo_Poly1 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228390 E-MTAB-4091:siGlo_Poly2 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989643 SAMEA3682494 E-MTAB-4091:siGlo_Poly2 siGlo_Poly2 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228391 E-MTAB-4091:siGlo_Poly3 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989644 SAMEA3682495 E-MTAB-4091:siGlo_Poly3 siGlo_Poly3 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228392 E-MTAB-4091:siGlo_Tot1 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989645 SAMEA3682496 E-MTAB-4091:siGlo_Tot1 siGlo_Tot1 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Whole cell lysate fraction ERX1228393 E-MTAB-4091:siGlo_Tot2 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989646 SAMEA3682497 E-MTAB-4091:siGlo_Tot2 siGlo_Tot2 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Whole cell lysate fraction ERX1228394 E-MTAB-4091:siGlo_Tot3 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989647 SAMEA3682498 E-MTAB-4091:siGlo_Tot3 siGlo_Tot3 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: Control siRNA rna interference Experimental Factor: Whole cell lysate fraction ERX1228395 E-MTAB-4091:sip54_Poly1 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989648 SAMEA3682499 E-MTAB-4091:sip54_Poly1 sip54_Poly1 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228396 E-MTAB-4091:sip54_Poly2 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989649 SAMEA3682500 E-MTAB-4091:sip54_Poly2 sip54_Poly2 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228397 E-MTAB-4091:sip54_Poly3 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989650 SAMEA3682501 E-MTAB-4091:sip54_Poly3 sip54_Poly3 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection HEK 293 cells were harvested in ice-cold PBS, lysed for 10 minutes in ice-cold polysome lysis buffer (20 mM HEPES pH 7.4, 250 mM KCl, 10 mM MgCl2, 5 mM DTT, 0.5 % (v/v) NP40) supplemented with EDTA-free protease inhibitor cocktail (Roche Diagnostics) and 20 units/mL RNaseOut (Promega). Cell lysates were centrifuged at 500 g for 5 min to eliminate nuclei. Supernatant corresponding to 106 cells was reserved for total RNA extraction, while the remaining sample (~8.106 cells) was separated through a 36 mL 10-50 % (w/v) sucrose gradient in polysome buffer (20 mM HEPES pH 7.4, 250 mM KCl, 20 mM MgCl2, 2mM DTT). After centrifugation at 26 000 rpm for 4 h at 4C in a SW-27 rotor (Beckman Coulter), 28 fractions were collected by upward displacement with the ISCO gradient fractionation system (Teledyne Osco) connected to a UV detector to continuously monitor the absorbance at 254 nm. Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Polysome preparation fraction ERX1228398 E-MTAB-4091:sip54_Tot1 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989651 SAMEA3682502 E-MTAB-4091:sip54_Tot1 sip54_Tot1 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Whole cell lysate fraction ERX1228399 E-MTAB-4091:sip54_Tot2 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989652 SAMEA3682503 E-MTAB-4091:sip54_Tot2 sip54_Tot2 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Whole cell lysate fraction ERX1228400 E-MTAB-4091:sip54_Tot3 ERP013387 E-MTAB-4091 Large-scale study of total and polysomial mRNA after DDX6 depletion in HEK293 cells ERS989653 SAMEA3682504 E-MTAB-4091:sip54_Tot3 sip54_Tot3 RNA-Seq TRANSCRIPTOMIC cDNA Human embryonic kidney HEK293 cells were maintained in DMEM supplemented with 10% (v/v) fetal calf serum. siRNA transfections were performed using Lipofectamin 2000 (Life Technologies, France) according to the manufacturer's protocol. Cells were harvested 48h post-transfection Total and polysomial RNA was extracted using the SV Total RNA Isolation System (Promega) according to the manufacturers instructions Library preparation was performed at the Ecole Normale Superieure Genomic Platform (Paris, France). Ribosomal RNA was depleted from 1 g of total or polysomial RNA using the Ribo-Zero kit Human/Mouse/Rat (Epicentre). Libraries were prepared using the strand specific RNASeq library preparation ScriptSeq V2 kit (Epicentre), and multiplexed by three on flow cell lanes. Illumina HiSeq 1500 Experimental Factor: DDX6 siRNA rna interference Experimental Factor: Whole cell lysate fraction