SRX876723 GSM1609377 SRP055009 SRS845425 GSM1609377 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609377 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609377 gds 301609377 GEO Accession GSM1609377 SRX876724 GSM1609378 SRP055009 SRS845424 GSM1609378 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609378 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609378 gds 301609378 GEO Accession GSM1609378 SRX876725 GSM1609379 SRP055009 SRS845423 GSM1609379 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609379 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609379 gds 301609379 GEO Accession GSM1609379 SRX876726 GSM1609380 SRP055009 SRS845421 GSM1609380 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609380 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609380 gds 301609380 GEO Accession GSM1609380 SRX876727 GSM1609381 SRP055009 SRS845420 GSM1609381 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609381 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609381 gds 301609381 GEO Accession GSM1609381 SRX876728 GSM1609382 SRP055009 SRS845422 GSM1609382 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609382 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609382 gds 301609382 GEO Accession GSM1609382 SRX876729 GSM1609383 SRP055009 SRS845418 GSM1609383 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609383 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609383 gds 301609383 GEO Accession GSM1609383 SRX876730 GSM1609384 SRP055009 SRS845419 GSM1609384 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609384 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609384 gds 301609384 GEO Accession GSM1609384 SRX876731 GSM1609385 SRP055009 SRS845417 GSM1609385 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609385 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609385 gds 301609385 GEO Accession GSM1609385 SRX876732 GSM1609386 SRP055009 SRS845415 GSM1609386 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609386 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609386 gds 301609386 GEO Accession GSM1609386 SRX876733 GSM1609387 SRP055009 SRS845412 GSM1609387 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609387 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609387 gds 301609387 GEO Accession GSM1609387 SRX876734 GSM1609388 SRP055009 SRS845416 GSM1609388 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609388 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609388 gds 301609388 GEO Accession GSM1609388 SRX876735 GSM1609389 SRP055009 SRS845414 GSM1609389 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609389 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609389 gds 301609389 GEO Accession GSM1609389 SRX876736 GSM1609390 SRP055009 SRS845413 GSM1609390 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609390 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609390 gds 301609390 GEO Accession GSM1609390 SRX876737 GSM1609391 SRP055009 SRS845410 GSM1609391 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609391 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609391 gds 301609391 GEO Accession GSM1609391 SRX876738 GSM1609392 SRP055009 SRS845411 GSM1609392 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609392 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609392 gds 301609392 GEO Accession GSM1609392 SRX876739 GSM1609393 SRP055009 SRS845409 GSM1609393 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609393 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609393 gds 301609393 GEO Accession GSM1609393 SRX876740 GSM1609394 SRP055009 SRS845406 GSM1609394 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609394 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609394 gds 301609394 GEO Accession GSM1609394 SRX876741 GSM1609395 SRP055009 SRS845405 GSM1609395 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609395 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609395 gds 301609395 GEO Accession GSM1609395 SRX876742 GSM1609396 SRP055009 SRS845404 GSM1609396 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609396 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609396 gds 301609396 GEO Accession GSM1609396 SRX876743 GSM1609397 SRP055009 SRS845408 GSM1609397 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609397 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609397 gds 301609397 GEO Accession GSM1609397 SRX876744 GSM1609398 SRP055009 SRS845403 GSM1609398 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609398 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609398 gds 301609398 GEO Accession GSM1609398 SRX876745 GSM1609399 SRP055009 SRS845407 GSM1609399 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609399 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609399 gds 301609399 GEO Accession GSM1609399 SRX876746 GSM1609400 SRP055009 SRS845402 GSM1609400 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609400 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609400 gds 301609400 GEO Accession GSM1609400 SRX876747 GSM1609401 SRP055009 SRS845401 GSM1609401 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609401 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609401 gds 301609401 GEO Accession GSM1609401 SRX876748 GSM1609402 SRP055009 SRS845399 GSM1609402 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609402 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609402 gds 301609402 GEO Accession GSM1609402 SRX876749 GSM1609403 SRP055009 SRS845396 GSM1609403 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609403 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609403 gds 301609403 GEO Accession GSM1609403 SRX876750 GSM1609404 SRP055009 SRS845397 GSM1609404 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609404 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609404 gds 301609404 GEO Accession GSM1609404 SRX876751 GSM1609405 SRP055009 SRS845395 GSM1609405 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609405 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609405 gds 301609405 GEO Accession GSM1609405 SRX876752 GSM1609406 SRP055009 SRS845394 GSM1609406 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609406 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609406 gds 301609406 GEO Accession GSM1609406 SRX876753 GSM1609407 SRP055009 SRS845392 GSM1609407 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609407 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609407 gds 301609407 GEO Accession GSM1609407 SRX876754 GSM1609408 SRP055009 SRS845391 GSM1609408 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609408 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609408 gds 301609408 GEO Accession GSM1609408 SRX876755 GSM1609409 SRP055009 SRS845390 GSM1609409 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609409 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609409 gds 301609409 GEO Accession GSM1609409 SRX876756 GSM1609410 SRP055009 SRS845400 GSM1609410 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609410 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609410 gds 301609410 GEO Accession GSM1609410 SRX876757 GSM1609411 SRP055009 SRS845398 GSM1609411 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609411 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609411 gds 301609411 GEO Accession GSM1609411 SRX876758 GSM1609412 SRP055009 SRS845389 GSM1609412 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609412 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609412 gds 301609412 GEO Accession GSM1609412 SRX876759 GSM1609413 SRP055009 SRS845388 GSM1609413 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609413 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609413 gds 301609413 GEO Accession GSM1609413 SRX876760 GSM1609414 SRP055009 SRS845393 GSM1609414 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609414 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609414 gds 301609414 GEO Accession GSM1609414 SRX876761 GSM1609415 SRP055009 SRS845386 GSM1609415 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609415 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609415 gds 301609415 GEO Accession GSM1609415 SRX876762 GSM1609416 SRP055009 SRS845385 GSM1609416 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609416 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609416 gds 301609416 GEO Accession GSM1609416 SRX876763 GSM1609417 SRP055009 SRS845387 GSM1609417 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609417 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609417 gds 301609417 GEO Accession GSM1609417 SRX876764 GSM1609418 SRP055009 SRS845384 GSM1609418 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609418 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609418 gds 301609418 GEO Accession GSM1609418 SRX876765 GSM1609419 SRP055009 SRS845383 GSM1609419 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609419 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609419 gds 301609419 GEO Accession GSM1609419 SRX876766 GSM1609420 SRP055009 SRS845379 GSM1609420 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609420 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609420 gds 301609420 GEO Accession GSM1609420 SRX876767 GSM1609421 SRP055009 SRS845381 GSM1609421 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609421 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609421 gds 301609421 GEO Accession GSM1609421 SRX876768 GSM1609422 SRP055009 SRS845382 GSM1609422 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609422 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609422 gds 301609422 GEO Accession GSM1609422 SRX876769 GSM1609423 SRP055009 SRS845377 GSM1609423 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609423 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609423 gds 301609423 GEO Accession GSM1609423 SRX876770 GSM1609424 SRP055009 SRS845380 GSM1609424 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609424 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609424 gds 301609424 GEO Accession GSM1609424 SRX876771 GSM1609425 SRP055009 SRS845376 GSM1609425 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609425 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609425 gds 301609425 GEO Accession GSM1609425 SRX876772 GSM1609426 SRP055009 SRS845375 GSM1609426 OTHER TRANSCRIPTOMIC other For ribosome profiling experiments, a 34% (Weight/Volume) sucrose cushion was used. 7 A260 Units of the cleared cell lysate were incubated with 300 Units of RNase T1 (Fermentas) and 500ng of RNaseA (Ambion) for 30 minutes at room temperature. RNase digestion was stopped with 20 mM Ribonucleoside Vanadyl Complex (NEB: S1402S). No RNase control included 20 mM Ribonucleoside Vanadyl Complex in cell lysis buffer to inhibit any endogenous RNase activity. The sample was ultracentrifuged in a TLA120.3 rotor at 4ºC for 4 h at 70,000 rpm. For ribosome profiling experiments, the pellet was resuspended in 700ul of Qiazol reagent from miRNeasy kit. The RNA was purified using manufacturer’s instructions. Purified RNA was 3’end dephosphorylated using 10U of T4 PNK (NEB) at 37C for 3 hours. Dephosphorylated RNA was heated to 80C for 90 seconds before loading onto 15% (Weight/Volume) polyacrylamide TBE-Urea gel that was prerun at 180V for 15min. Electrophoresis was carried out for ~1.5hr at 180V. Custom RNA oligos were used to determine the 26-34nt size range on the gel and was excised on a DarkReader Transilluminator (Clare Chemical Research). Excised gel pieces were placed in GeBAflex electroelution tubes with 8 kDA molecular weight cutoff (Gerard Biotech). Electroelution was carried out at 120V for 90min, and the eluate was filtered through Spin-X 0.22um Cellulose Acetate centrifuge filter tubes (Sigma). 300 mM sodium acetate pH 5.5, 10 mM MgCl2, and 22.5 μg of GlycoBlue (Life Technologies) was added to filtrate. Equal volume of 100% isopropanol was used for precipitation at -20°C overnight. RNA was pelleted by centrifugation at 21000g at 4C. RNA pellet was washed once with cold 75% ethanol and resuspended in 6ul of nuclease free water. NEBNext Small RNA Library preparation kit was used to convert the isolated RNA fragments into Illumina sequencing library using manufacturer’s instructions except for the choice of 30C for 3hrs for all ligation reactions. Illumina HiSeq 2000 GEO Sample GSM1609426 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609426 gds 301609426 GEO Accession GSM1609426 SRX876773 GSM1609427 SRP055009 SRS845374 GSM1609427 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609427 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609427 gds 301609427 GEO Accession GSM1609427 SRX876774 GSM1609428 SRP055009 SRS845378 GSM1609428 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609428 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609428 gds 301609428 GEO Accession GSM1609428 SRX876775 GSM1609429 SRP055009 SRS845373 GSM1609429 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609429 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609429 gds 301609429 GEO Accession GSM1609429 SRX876776 GSM1609430 SRP055009 SRS845372 GSM1609430 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609430 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609430 gds 301609430 GEO Accession GSM1609430 SRX876777 GSM1609431 SRP055009 SRS845371 GSM1609431 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609431 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609431 gds 301609431 GEO Accession GSM1609431 SRX876778 GSM1609432 SRP055009 SRS845369 GSM1609432 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609432 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609432 gds 301609432 GEO Accession GSM1609432 SRX876779 GSM1609433 SRP055009 SRS845367 GSM1609433 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609433 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609433 gds 301609433 GEO Accession GSM1609433 SRX876780 GSM1609434 SRP055009 SRS845366 GSM1609434 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609434 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609434 gds 301609434 GEO Accession GSM1609434 SRX876781 GSM1609435 SRP055009 SRS845370 GSM1609435 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609435 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609435 gds 301609435 GEO Accession GSM1609435 SRX876782 GSM1609436 SRP055009 SRS845365 GSM1609436 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609436 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609436 gds 301609436 GEO Accession GSM1609436 SRX876783 GSM1609437 SRP055009 SRS845368 GSM1609437 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609437 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609437 gds 301609437 GEO Accession GSM1609437 SRX876784 GSM1609438 SRP055009 SRS845364 GSM1609438 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609438 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609438 gds 301609438 GEO Accession GSM1609438 SRX876785 GSM1609439 SRP055009 SRS845363 GSM1609439 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609439 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609439 gds 301609439 GEO Accession GSM1609439 SRX876786 GSM1609440 SRP055009 SRS845362 GSM1609440 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609440 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609440 gds 301609440 GEO Accession GSM1609440 SRX876787 GSM1609441 SRP055009 SRS845359 GSM1609441 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609441 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609441 gds 301609441 GEO Accession GSM1609441 SRX876788 GSM1609442 SRP055009 SRS845361 GSM1609442 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609442 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609442 gds 301609442 GEO Accession GSM1609442 SRX876789 GSM1609443 SRP055009 SRS845360 GSM1609443 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609443 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609443 gds 301609443 GEO Accession GSM1609443 SRX876790 GSM1609444 SRP055009 SRS845358 GSM1609444 RNA-Seq TRANSCRIPTOMIC cDNA For RNA sequencing experiments, Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions (Lifetechnologies), then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen, Valencia, CA). RNA integrity was checked with a Bioanalyzer (Agilent, Santa Clara CA) and only samples with an RNA integrity number (RIN) of > 9.5 were subsequently subjected to poly-A-selection. For poly-A selection, 10 μg of purified total RNA were enriched by performing two cycles of selection using the Dynabeads mRNA Purification Kit (Life Technologies). For RNA sequencing experiments, stranded libraries were prepared following the dUTP protocol (Parkhomchuk et al., 2009). In brief: ~100 ng of poly-A-selected RNA were fragmented with 10 x fragmentation buffer (Life Technologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For the second-strand synthesis dTTP was replaced with dUTP. The cDNA was end-repaired and phosphorylated with the End-It kit from Epicentre (ER0720). After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina TruSeq adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil N-glycosylase (UNG) (Life Technologies, N8080096). Illumina HiSeq 2000 GEO Sample GSM1609444 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1609444 gds 301609444 GEO Accession GSM1609444