SRX3481638 RD9_8ips_nt_pl_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767468 SAMN07351624 RD9_8ips_nt_pl_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481639 RD9_8ips_nt_em_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767469 SAMN07351623 RD9_8ips_nt_em_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481640 RD9_6ips_nt_pl_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767470 SAMN07351622 RD9_6ips_nt_pl_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481641 RD9_6ips_nt_em_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767471 SAMN07351621 RD9_6ips_nt_em_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481642 1631_3pl_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767473 SAMN07109443 1631_3pl_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481643 1631_2pl_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767472 SAMN07109442 1631_2pl_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481644 1631_3em_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767474 SAMN07109427 1631_3em_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481645 1631_2em_lnc SRP107099 PRJNA357875 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Firstly, ribosomal RNA was removed by Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNAbyNEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer s recommendations. Briefly, fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer 5X . First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase RNaseH- . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPswith dTTP were replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3 ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 l USER Enzyme (NEB USA) wasused with size-selected, adaptor-ligated cDNA at 37 Cfor 15 min followed by 5 min at 95 C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XPsystem) and library quality was assessed on the Agilent Bioanalyzer 2100 system. SRS2767475 SAMN07109426 1631_2em_lnc ncRNA-Seq TRANSCRIPTOMIC RANDOM PCR HiSeq X Ten SRX3481646 1DNT_2pl_wgbs SRP107099 A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. SRS2767476 1DNT_2pl_wgbs Bisulfite-Seq GENOMIC RANDOM PCR 300 0 Application Read Forward 1 1 Application Read Reverse 151 HiSeq X Ten SRX3481647 1DNT_5em_wgbs SRP107099 PRJNA357875 A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. SRS2767477 SAMN07125693 1DNT_5em_wgbs Bisulfite-Seq GENOMIC RANDOM PCR HiSeq X Ten