SRX5624281 GSM3702256 SRP190145 SRS4569413 GSM3702256 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702256 GSM3702256 GEO Accession GSM3702256 SRX5624282 GSM3702257 SRP190145 SRS4569414 GSM3702257 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702257 GSM3702257 GEO Accession GSM3702257 SRX5624283 GSM3702258 SRP190145 SRS4569415 GSM3702258 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702258 GSM3702258 GEO Accession GSM3702258 SRX5624284 GSM3702259 SRP190145 SRS4569416 GSM3702259 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702259 GSM3702259 GEO Accession GSM3702259 SRX5624285 GSM3702260 SRP190145 SRS4569417 GSM3702260 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702260 GSM3702260 GEO Accession GSM3702260 SRX5624286 GSM3702261 SRP190145 SRS4569418 GSM3702261 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702261 GSM3702261 GEO Accession GSM3702261 SRX5624287 GSM3702262 SRP190145 SRS4569419 GSM3702262 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702262 GSM3702262 GEO Accession GSM3702262 SRX5624288 GSM3702263 SRP190145 SRS4569420 GSM3702263 OTHER TRANSCRIPTOMIC other 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702263 GSM3702263 GEO Accession GSM3702263 SRX5624289 GSM3702264 SRP190145 SRS4569421 GSM3702264 RNA-Seq TRANSCRIPTOMIC cDNA 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702264 GSM3702264 GEO Accession GSM3702264 SRX5624290 GSM3702265 SRP190145 SRS4569422 GSM3702265 RNA-Seq TRANSCRIPTOMIC cDNA 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702265 GSM3702265 GEO Accession GSM3702265 SRX5624291 GSM3702266 SRP190145 SRS4569423 GSM3702266 RNA-Seq TRANSCRIPTOMIC cDNA 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702266 GSM3702266 GEO Accession GSM3702266 SRX5624292 GSM3702267 SRP190145 SRS4569424 GSM3702267 RNA-Seq TRANSCRIPTOMIC cDNA 293T sh-Scramble and sh-YTHDC2 Cells were lysed in lysis buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2, 1% Triton X-100) containing CHX (100 µg ml-1),The supernatant was collected and subjected to sucrose gradient sedimentation. For RNA-seq, 12 µg Trizol extracted total RNAs were fragmentated by using freshly prepared RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2) and heating at 94°C for 5 min, followed by adding 1 µl 0.5 M EDTA to terminate. For Ribo-seq, *E. coli* RNase I (Ambion) was added into the pooled fractions from ribosome profiling (100 U per 100 µl) and incubated at 4 °C for 1 hr to convert the polysome into monosome. RNase I digested RNA extracts (Ribo-seq) and fragmented RNAs (RNA-seq) were dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase_In and 20 U T4 polynucleotide kinase). The products were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions in the gel corresponding to 40-60 nt (for RNA-seq) or 25-35 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer (300 mM NaOAc, pH 5.5, 1 mM EDTA, 0.1 U ml-1 SUPERase_In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation. Purified RNA fragments were re-suspended in nuclease-free water. 0.15 μg linker was added to the RNA fragments, heated at 70°C for 90 s and then cooled to room temperature, followed by ligation for 3 hrs at at 22°C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase_In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 65-85 nt (for RNA-seq) or 50-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA elution buffer, purified RNA fragments were re-suspended in nuclease-free water. The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75°C for 5 min, followed by incubation on ice for 3 min. The reaction mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer's instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel as described earlier. The extended first-strand product band was expected to be approximately 200 nt, and the corresponding region was excised. The cDNA was recovered by gel elution buffer (300 mM NaCl, 1 mM EDTA). First-strand cDNA was circularized in 20 μl of reaction containing 1× CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr, and the reaction was heat inactivated at 80 °C for 10 min, then was precipitated by ethanol. Circular template was amplified by PCR by using the Phusion high-fidelity (HF) enzyme (NEB) according to the manufacturer's instructions. PCR products were separated on a nondenaturing 8% polyacrylamide TBE gel as described earlier. Expected DNA at 180 bp was excised and recovered as described earlier. After quantification by Agilent BioAnalyzer DNA 1000 assay, equal amounts of barcoded samples were pooled into one sample. Approximately 5 pM mixed DNA samples were used for cluster generation followed by sequencing by using sequencing primer 5'-CGACAGGTTCAGAGTTCTACAGTCCGACGATC-3' (Illumina HiSeq). Illumina HiSeq 2500 gds 303702267 GSM3702267 GEO Accession GSM3702267