SRX1522529 GSM2033742 SRP068236 SRS1240657 GSM2033742 miRNA-Seq TRANSCRIPTOMIC size fractionation For Ago-APPs, 100 µg of the GST-tagged TNRC6B 599-683 peptide were coupled to Glutathione Sepharose beads for 3 h at 4°C. Cells were washed with cold PBS and lysed in 1 ml of lysis buffer [25mM Tris (pH 7.5),150mM KCl, 0.5% (v/v) NP-40, 2mM EDTA, 1mM NaF, 1mM DTT and 0.5mM AEBSF]. The lysates were cleared by centrifugation at 17,000xg for 30 min, before addition to the beads. After 3 h of rotation at 4°C, the beads were washed four times with wash buffer [50mM Tris–HCl (pH 7.5), 300mM KCl,1mM MgCl2 and 0.5% (v/v) NP-40] and once with PBS. For RNA extraction 200 µl proteinase K buffer [200mM Tris (pH 7.5), 300mM NaCl, 25mM EDTA, 2% SDS] containing 0.2 mg/ml proteinase K were added. The samples were incubated 30 min at 50°C, the RNA was then isolated with phenol/chloroform/isoamyl alcohol. Input samples were prepared by extracting total RNA directly from an aliquot of the lysates using TRIzol according to the manufacturer’s instructions. In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA-sized inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements. Illumina MiSeq gds 302033742 GEO Accession GSM2033742 SRX1522530 GSM2033745 SRP068236 SRS1240658 GSM2033745 miRNA-Seq TRANSCRIPTOMIC size fractionation For Ago-APPs, 100 µg of the GST-tagged TNRC6B 599-683 peptide were coupled to Glutathione Sepharose beads for 3 h at 4°C. Cells were washed with cold PBS and lysed in 1 ml of lysis buffer [25mM Tris (pH 7.5),150mM KCl, 0.5% (v/v) NP-40, 2mM EDTA, 1mM NaF, 1mM DTT and 0.5mM AEBSF]. The lysates were cleared by centrifugation at 17,000xg for 30 min, before addition to the beads. After 3 h of rotation at 4°C, the beads were washed four times with wash buffer [50mM Tris–HCl (pH 7.5), 300mM KCl,1mM MgCl2 and 0.5% (v/v) NP-40] and once with PBS. For RNA extraction 200 µl proteinase K buffer [200mM Tris (pH 7.5), 300mM NaCl, 25mM EDTA, 2% SDS] containing 0.2 mg/ml proteinase K were added. The samples were incubated 30 min at 50°C, the RNA was then isolated with phenol/chloroform/isoamyl alcohol. Input samples were prepared by extracting total RNA directly from an aliquot of the lysates using TRIzol according to the manufacturer’s instructions. In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA-sized inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements. Illumina MiSeq gds 302033745 GEO Accession GSM2033745 SRX1522531 GSM2033747 SRP068236 SRS1240659 GSM2033747 miRNA-Seq TRANSCRIPTOMIC size fractionation For Ago-APPs, 100 µg of the GST-tagged TNRC6B 599-683 peptide were coupled to Glutathione Sepharose beads for 3 h at 4°C. Cells were washed with cold PBS and lysed in 1 ml of lysis buffer [25mM Tris (pH 7.5),150mM KCl, 0.5% (v/v) NP-40, 2mM EDTA, 1mM NaF, 1mM DTT and 0.5mM AEBSF]. The lysates were cleared by centrifugation at 17,000xg for 30 min, before addition to the beads. After 3 h of rotation at 4°C, the beads were washed four times with wash buffer [50mM Tris–HCl (pH 7.5), 300mM KCl,1mM MgCl2 and 0.5% (v/v) NP-40] and once with PBS. For RNA extraction 200 µl proteinase K buffer [200mM Tris (pH 7.5), 300mM NaCl, 25mM EDTA, 2% SDS] containing 0.2 mg/ml proteinase K were added. The samples were incubated 30 min at 50°C, the RNA was then isolated with phenol/chloroform/isoamyl alcohol. Input samples were prepared by extracting total RNA directly from an aliquot of the lysates using TRIzol according to the manufacturer’s instructions. In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA-sized inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements. Illumina MiSeq gds 302033747 GEO Accession GSM2033747 SRX1522532 GSM2033749 SRP068236 SRS1240656 GSM2033749 miRNA-Seq TRANSCRIPTOMIC size fractionation For Ago-APPs, 100 µg of the GST-tagged TNRC6B 599-683 peptide were coupled to Glutathione Sepharose beads for 3 h at 4°C. Cells were washed with cold PBS and lysed in 1 ml of lysis buffer [25mM Tris (pH 7.5),150mM KCl, 0.5% (v/v) NP-40, 2mM EDTA, 1mM NaF, 1mM DTT and 0.5mM AEBSF]. The lysates were cleared by centrifugation at 17,000xg for 30 min, before addition to the beads. After 3 h of rotation at 4°C, the beads were washed four times with wash buffer [50mM Tris–HCl (pH 7.5), 300mM KCl,1mM MgCl2 and 0.5% (v/v) NP-40] and once with PBS. For RNA extraction 200 µl proteinase K buffer [200mM Tris (pH 7.5), 300mM NaCl, 25mM EDTA, 2% SDS] containing 0.2 mg/ml proteinase K were added. The samples were incubated 30 min at 50°C, the RNA was then isolated with phenol/chloroform/isoamyl alcohol. Input samples were prepared by extracting total RNA directly from an aliquot of the lysates using TRIzol according to the manufacturer’s instructions. In short, an adenylated adapter was ligated to the 3’ end of the total RNA and APP-enriched RNA by a truncated T4 RNA Ligase 2, followed by the ligation of a 5’ RNA-adapter by T4 RNA Ligase 1 (NEB). After reverse-transcription using a specific primer, the cDNA was amplified by PCR, gel-fractionated and bands or regions corresponding to miRNA-sized inserts were cut out. PCR products from these gel slices were eluted in elution buffer, precipitated and dissolved in water. The quality of the libraries was assessed by qPCR and Bioanalyzer measurements. Illumina MiSeq gds 302033749 GEO Accession GSM2033749