poly a rna  (New England Biolabs)


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    Name:
    RNA 5’ Pyrophosphohydrolase RppH
    Description:
    RNA 5 Pyrophosphohydrolase RppH 200 units
    Catalog Number:
    m0356s
    Price:
    93
    Size:
    200 units
    Category:
    Other Enzymes
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    Structured Review

    New England Biolabs poly a rna
    RNA 5’ Pyrophosphohydrolase RppH
    RNA 5 Pyrophosphohydrolase RppH 200 units
    https://www.bioz.com/result/poly a rna/product/New England Biolabs
    Average 92 stars, based on 117 article reviews
    Price from $9.99 to $1999.99
    poly a rna - by Bioz Stars, 2020-07
    92/100 stars

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    Related Articles

    GWAS:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    RNA Sequencing Assay:

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

    Polyacrylamide Gel Electrophoresis:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

    Protease Inhibitor:

    Article Title: A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)
    Article Snippet: .. CAUTION: DEPC is toxic and harmful DEPC treated ddH2 O (0.1% v/v) 4 M KCl (see Note 1) 5 M NaCl (see Note 1) 1M MgCl2 (see Note 1) 10% (v/v) Triton X-100 (see Note 2) 2% (v/v) Sarkosyl (Sigma-Aldrich, cat. no. L5125) (see Note 2) 2% (v/v) Tween-20 (see Note 2) 10 % Igepal® CA-630 (Millipore Sigma cat. no. I8896) (see Note 2) 0.1 M DTT (see Note 2) 1 M Sucrose (see Note 2) 0.5 M EDTA, pH 8.0 (see Note 2) 0.1 M EGTA, pH 8.0 (see Note 2) Tris-Cl, pH 6.8 (See Note 2) Tris-Cl, pH 7.4 (See Note 2) Tris-Cl, pH 8.0 (See Note 2) Glycerol 1 N NaOH 100% Ethanol 75% Ethanol Biotin-11-CTP 10 mM (PerkinElmer, cat. no. NEL542001EA) Biotin-11-UTP 10 mM (PerkinElmer, cat. no. NEL543001EA) Biotin-11-GTP 10 mM (PerkinElmer, cat. no. NEL545001EA) Biotin-11-ATP 10 mM (PerkinElmer, cat. no. NEL544001EA) GTP, 100 mM (Roche, cat. no. 11277057001) ATP, 100 mM (Roche, cat. no. 11277057001) Trypan Blue Dynabeads™ MyOne™ Streptavidin C1 Beads (Invitrogen, cat. no. 65002) TRIzol™ Reagent (Invitrogen, cat. no. 15596018) TRIzol™ LS Reagent (Invitrogen, cat. no. 10296028) (optional, see Note 3) Total RNA Purification Kit (Norgen, cat. no. 37500) (optional, see Note 3) Chloroform GlycoBlue™ (Invitrogen, cat. no. AM9515) SUPERase-In™ RNase Inhibitor (20 U/µL) (Invitrogen, cat. no. AM2694) Pierce™ Protease Inhibitor Tablets (Thermo Scientific cat. no. A32963) T4 RNA Ligase (10 U/µL), supplied with 10X T4 RNA ligase buffer, 10 mM ATP and 50% (w/v) PEG8000 (NEB cat. no. M0204S) RNA 5’ pyrophosphohydrolase (RppH; 5 U/µL) (NEB, cat. no. M0356S) 10X ThermoPol Reaction Buffer (NEB, cat. no. B9004S) T4 polynucleotide kinase (PNK; 10 U/µL), supplied with 10X PNK buffer (NEB, cat. no. M0201) Maxima H Minus Reverse Transcriptase (200 U/µL) (Thermo Scientific, cat. no. EP0751) dNTP mix, 12.5mM each (Roche, cat. no. 03622614001) Q5® High-Fidelity DNA Polymerase, supplied with 5X Q5 Reaction Buffer and 5X High GC-Enhancer (NEB cat. no. M0491S) Micro Bio-Spin™ RNase free P-30 Gel Columns (Bio-Rad, cat. no. 7326250) (optional, see Note 3) RNA and DNA oligos (IDT DNA) (see and Notes 4–6) Agencourt AMPure XP SPRI beads (Beckman-Coulter, cat. no. A63880) SYBR Gold stain (Invitrogen, cat. no. S11494) Costar® Spin-X® 0.22 µm Centrifuge Tube Filters (Corning, cat. no. 1860) SsoAdvanced Universal SYBR Green Supermix (BioRad, cat. no. 1725270) .. 2.2 Buffers Permeabilization Buffer: 10 mM Tris-Cl [pH 8.0], 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2 , 1 mM EGTA, 0.1% (v/v) Igepal, 0.5 mM DTT, 0.05% (v/v) Tween-20, and 10% (v/v) Glycerol in DEPC H2 O.

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

    Purification:

    Article Title: A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)
    Article Snippet: .. CAUTION: DEPC is toxic and harmful DEPC treated ddH2 O (0.1% v/v) 4 M KCl (see Note 1) 5 M NaCl (see Note 1) 1M MgCl2 (see Note 1) 10% (v/v) Triton X-100 (see Note 2) 2% (v/v) Sarkosyl (Sigma-Aldrich, cat. no. L5125) (see Note 2) 2% (v/v) Tween-20 (see Note 2) 10 % Igepal® CA-630 (Millipore Sigma cat. no. I8896) (see Note 2) 0.1 M DTT (see Note 2) 1 M Sucrose (see Note 2) 0.5 M EDTA, pH 8.0 (see Note 2) 0.1 M EGTA, pH 8.0 (see Note 2) Tris-Cl, pH 6.8 (See Note 2) Tris-Cl, pH 7.4 (See Note 2) Tris-Cl, pH 8.0 (See Note 2) Glycerol 1 N NaOH 100% Ethanol 75% Ethanol Biotin-11-CTP 10 mM (PerkinElmer, cat. no. NEL542001EA) Biotin-11-UTP 10 mM (PerkinElmer, cat. no. NEL543001EA) Biotin-11-GTP 10 mM (PerkinElmer, cat. no. NEL545001EA) Biotin-11-ATP 10 mM (PerkinElmer, cat. no. NEL544001EA) GTP, 100 mM (Roche, cat. no. 11277057001) ATP, 100 mM (Roche, cat. no. 11277057001) Trypan Blue Dynabeads™ MyOne™ Streptavidin C1 Beads (Invitrogen, cat. no. 65002) TRIzol™ Reagent (Invitrogen, cat. no. 15596018) TRIzol™ LS Reagent (Invitrogen, cat. no. 10296028) (optional, see Note 3) Total RNA Purification Kit (Norgen, cat. no. 37500) (optional, see Note 3) Chloroform GlycoBlue™ (Invitrogen, cat. no. AM9515) SUPERase-In™ RNase Inhibitor (20 U/µL) (Invitrogen, cat. no. AM2694) Pierce™ Protease Inhibitor Tablets (Thermo Scientific cat. no. A32963) T4 RNA Ligase (10 U/µL), supplied with 10X T4 RNA ligase buffer, 10 mM ATP and 50% (w/v) PEG8000 (NEB cat. no. M0204S) RNA 5’ pyrophosphohydrolase (RppH; 5 U/µL) (NEB, cat. no. M0356S) 10X ThermoPol Reaction Buffer (NEB, cat. no. B9004S) T4 polynucleotide kinase (PNK; 10 U/µL), supplied with 10X PNK buffer (NEB, cat. no. M0201) Maxima H Minus Reverse Transcriptase (200 U/µL) (Thermo Scientific, cat. no. EP0751) dNTP mix, 12.5mM each (Roche, cat. no. 03622614001) Q5® High-Fidelity DNA Polymerase, supplied with 5X Q5 Reaction Buffer and 5X High GC-Enhancer (NEB cat. no. M0491S) Micro Bio-Spin™ RNase free P-30 Gel Columns (Bio-Rad, cat. no. 7326250) (optional, see Note 3) RNA and DNA oligos (IDT DNA) (see and Notes 4–6) Agencourt AMPure XP SPRI beads (Beckman-Coulter, cat. no. A63880) SYBR Gold stain (Invitrogen, cat. no. S11494) Costar® Spin-X® 0.22 µm Centrifuge Tube Filters (Corning, cat. no. 1860) SsoAdvanced Universal SYBR Green Supermix (BioRad, cat. no. 1725270) .. 2.2 Buffers Permeabilization Buffer: 10 mM Tris-Cl [pH 8.0], 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2 , 1 mM EGTA, 0.1% (v/v) Igepal, 0.5 mM DTT, 0.05% (v/v) Tween-20, and 10% (v/v) Glycerol in DEPC H2 O.

    SYBR Green Assay:

    Article Title: A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)
    Article Snippet: .. CAUTION: DEPC is toxic and harmful DEPC treated ddH2 O (0.1% v/v) 4 M KCl (see Note 1) 5 M NaCl (see Note 1) 1M MgCl2 (see Note 1) 10% (v/v) Triton X-100 (see Note 2) 2% (v/v) Sarkosyl (Sigma-Aldrich, cat. no. L5125) (see Note 2) 2% (v/v) Tween-20 (see Note 2) 10 % Igepal® CA-630 (Millipore Sigma cat. no. I8896) (see Note 2) 0.1 M DTT (see Note 2) 1 M Sucrose (see Note 2) 0.5 M EDTA, pH 8.0 (see Note 2) 0.1 M EGTA, pH 8.0 (see Note 2) Tris-Cl, pH 6.8 (See Note 2) Tris-Cl, pH 7.4 (See Note 2) Tris-Cl, pH 8.0 (See Note 2) Glycerol 1 N NaOH 100% Ethanol 75% Ethanol Biotin-11-CTP 10 mM (PerkinElmer, cat. no. NEL542001EA) Biotin-11-UTP 10 mM (PerkinElmer, cat. no. NEL543001EA) Biotin-11-GTP 10 mM (PerkinElmer, cat. no. NEL545001EA) Biotin-11-ATP 10 mM (PerkinElmer, cat. no. NEL544001EA) GTP, 100 mM (Roche, cat. no. 11277057001) ATP, 100 mM (Roche, cat. no. 11277057001) Trypan Blue Dynabeads™ MyOne™ Streptavidin C1 Beads (Invitrogen, cat. no. 65002) TRIzol™ Reagent (Invitrogen, cat. no. 15596018) TRIzol™ LS Reagent (Invitrogen, cat. no. 10296028) (optional, see Note 3) Total RNA Purification Kit (Norgen, cat. no. 37500) (optional, see Note 3) Chloroform GlycoBlue™ (Invitrogen, cat. no. AM9515) SUPERase-In™ RNase Inhibitor (20 U/µL) (Invitrogen, cat. no. AM2694) Pierce™ Protease Inhibitor Tablets (Thermo Scientific cat. no. A32963) T4 RNA Ligase (10 U/µL), supplied with 10X T4 RNA ligase buffer, 10 mM ATP and 50% (w/v) PEG8000 (NEB cat. no. M0204S) RNA 5’ pyrophosphohydrolase (RppH; 5 U/µL) (NEB, cat. no. M0356S) 10X ThermoPol Reaction Buffer (NEB, cat. no. B9004S) T4 polynucleotide kinase (PNK; 10 U/µL), supplied with 10X PNK buffer (NEB, cat. no. M0201) Maxima H Minus Reverse Transcriptase (200 U/µL) (Thermo Scientific, cat. no. EP0751) dNTP mix, 12.5mM each (Roche, cat. no. 03622614001) Q5® High-Fidelity DNA Polymerase, supplied with 5X Q5 Reaction Buffer and 5X High GC-Enhancer (NEB cat. no. M0491S) Micro Bio-Spin™ RNase free P-30 Gel Columns (Bio-Rad, cat. no. 7326250) (optional, see Note 3) RNA and DNA oligos (IDT DNA) (see and Notes 4–6) Agencourt AMPure XP SPRI beads (Beckman-Coulter, cat. no. A63880) SYBR Gold stain (Invitrogen, cat. no. S11494) Costar® Spin-X® 0.22 µm Centrifuge Tube Filters (Corning, cat. no. 1860) SsoAdvanced Universal SYBR Green Supermix (BioRad, cat. no. 1725270) .. 2.2 Buffers Permeabilization Buffer: 10 mM Tris-Cl [pH 8.0], 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2 , 1 mM EGTA, 0.1% (v/v) Igepal, 0.5 mM DTT, 0.05% (v/v) Tween-20, and 10% (v/v) Glycerol in DEPC H2 O.

    Immunoprecipitation:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    Incubation:

    Article Title: ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
    Article Snippet: .. The mixture was incubated at 37°C for an additional 5 h. For quantification of cap m6 Am , 100 ng poly(A) RNA was decapped with 20 units of RNA 5′pyrophosphohydrolase (RppH; M0356; New England Biolabs) in 1×Thermopol buffer (B9004S; New England Biolabs) for 3 h at 37°C, and then treated with Nuclease P1 and alkaline phosphatase as described above. ..

    Article Title: Nucleotide Resolution Comparison of Transcription of Human Cytomegalovirus and Host Genomes Reveals Universal Use of RNA Polymerase II Elongation Control Driven by Dissimilar Core Promoter Elements
    Article Snippet: .. All samples were incubated at 37°C for 1 h with 10 µl 2× RppH mix (0.5 U/µl RNA 5′ pyrophosphohydrolase [NEB M0356], 2× ThermoPol buffer, and 1 U/µl SUPERase-In). .. PRO-Seq samples were then incubated at 37°C for 1 h with 80 µl 5/4× T4 polynucleotide kinase (PNK) mix (0.313 U/µl T4 PNK [NEB M0201], 5/4× T4 PNK buffer, 1.25 mM ATP, and 0.625 U/µl SUPERase-In).

    Expressing:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    Staining:

    Article Title: A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)
    Article Snippet: .. CAUTION: DEPC is toxic and harmful DEPC treated ddH2 O (0.1% v/v) 4 M KCl (see Note 1) 5 M NaCl (see Note 1) 1M MgCl2 (see Note 1) 10% (v/v) Triton X-100 (see Note 2) 2% (v/v) Sarkosyl (Sigma-Aldrich, cat. no. L5125) (see Note 2) 2% (v/v) Tween-20 (see Note 2) 10 % Igepal® CA-630 (Millipore Sigma cat. no. I8896) (see Note 2) 0.1 M DTT (see Note 2) 1 M Sucrose (see Note 2) 0.5 M EDTA, pH 8.0 (see Note 2) 0.1 M EGTA, pH 8.0 (see Note 2) Tris-Cl, pH 6.8 (See Note 2) Tris-Cl, pH 7.4 (See Note 2) Tris-Cl, pH 8.0 (See Note 2) Glycerol 1 N NaOH 100% Ethanol 75% Ethanol Biotin-11-CTP 10 mM (PerkinElmer, cat. no. NEL542001EA) Biotin-11-UTP 10 mM (PerkinElmer, cat. no. NEL543001EA) Biotin-11-GTP 10 mM (PerkinElmer, cat. no. NEL545001EA) Biotin-11-ATP 10 mM (PerkinElmer, cat. no. NEL544001EA) GTP, 100 mM (Roche, cat. no. 11277057001) ATP, 100 mM (Roche, cat. no. 11277057001) Trypan Blue Dynabeads™ MyOne™ Streptavidin C1 Beads (Invitrogen, cat. no. 65002) TRIzol™ Reagent (Invitrogen, cat. no. 15596018) TRIzol™ LS Reagent (Invitrogen, cat. no. 10296028) (optional, see Note 3) Total RNA Purification Kit (Norgen, cat. no. 37500) (optional, see Note 3) Chloroform GlycoBlue™ (Invitrogen, cat. no. AM9515) SUPERase-In™ RNase Inhibitor (20 U/µL) (Invitrogen, cat. no. AM2694) Pierce™ Protease Inhibitor Tablets (Thermo Scientific cat. no. A32963) T4 RNA Ligase (10 U/µL), supplied with 10X T4 RNA ligase buffer, 10 mM ATP and 50% (w/v) PEG8000 (NEB cat. no. M0204S) RNA 5’ pyrophosphohydrolase (RppH; 5 U/µL) (NEB, cat. no. M0356S) 10X ThermoPol Reaction Buffer (NEB, cat. no. B9004S) T4 polynucleotide kinase (PNK; 10 U/µL), supplied with 10X PNK buffer (NEB, cat. no. M0201) Maxima H Minus Reverse Transcriptase (200 U/µL) (Thermo Scientific, cat. no. EP0751) dNTP mix, 12.5mM each (Roche, cat. no. 03622614001) Q5® High-Fidelity DNA Polymerase, supplied with 5X Q5 Reaction Buffer and 5X High GC-Enhancer (NEB cat. no. M0491S) Micro Bio-Spin™ RNase free P-30 Gel Columns (Bio-Rad, cat. no. 7326250) (optional, see Note 3) RNA and DNA oligos (IDT DNA) (see and Notes 4–6) Agencourt AMPure XP SPRI beads (Beckman-Coulter, cat. no. A63880) SYBR Gold stain (Invitrogen, cat. no. S11494) Costar® Spin-X® 0.22 µm Centrifuge Tube Filters (Corning, cat. no. 1860) SsoAdvanced Universal SYBR Green Supermix (BioRad, cat. no. 1725270) .. 2.2 Buffers Permeabilization Buffer: 10 mM Tris-Cl [pH 8.0], 10 mM KCl, 250 mM Sucrose, 5 mM MgCl2 , 1 mM EGTA, 0.1% (v/v) Igepal, 0.5 mM DTT, 0.05% (v/v) Tween-20, and 10% (v/v) Glycerol in DEPC H2 O.

    RNA Binding Assay:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    Recombinant:

    Article Title: Landscape and Regulation of m6A and m6Am Methylome across Human and Mouse Tissues.
    Article Snippet: .. KEY RESOURCES TABLE REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-m6A polyclonal antibody Millipore Cat# ABE572 Chemicals, Peptides, and Recombinant Proteins DMEM GIBCO Cat# 11965 FBS GIBCO Cat# 10438-026 Pen/Strep GIBCO Cat# 15140 TRIzol Reagent Invitrogen Cat# 15596018 Nuclease P1 Sigma Cat# N8630 rSAP NEB Cat# M0371S Magnesium RNA fragmentation buffer NEB Cat# E6150S DNase I NEB Cat# M0303L RiboLock RNase Inhibitor Thermo Fisher Cat# EO0381 RppH NEB Cat# M0356S Dynabeads Protein G for Immunoprecipitation Thermo Fisher Cat# 10004D Dynabeads Protein A for Immunoprecipitation Thermo Fisher Cat# 10002D RNasin Plus RNase Inhibitor Promega Cat# N2615 N6-Methyladenosine 50-monophosphate sodium salt Sigma Cat# M2780 Critical Commercial Assays SMARTer Stranded Total RNA-SeqKit v2 - Pico Input Mammalian Takara - Clontech Cat# 634413 RevertAid First Strand cDNA Synthesis Kit Thermo Fisher Cat# K1622 Deposited Data m6A-seq data for human tissues and cell lines This paper GSA: CRA001315 m6A-seq data for mouse tissues This paper GSA: CRA001962 Protein expression data Human Proteome Map (HPM) http://www.humanproteomemap.org/ GTEx data Genotype-Tissue Expression (GTEx) https://gtexportal.org/home/ miRNA target site miRNA seed region miRbase http://www.mirbase.org miRNA target site starBase v3.0 http://starbase.sysu.edu.cn/index.php Human miRNA expression data miRmine http://guanlab.ccmb.med.umich.edu/mirmine/ rRNA of human mouse NCBI https://www.ncbi.nlm.nih.gov/gene/ Transcriptome reference under hg19 mm10 Refseq annotation UCSC table browser http://genome.ucsc.edu/cgi-bin/hgTables lncRNA reference LNCipedia https://lncipedia.org/download Orthologous gene annotation MGI http://www.informatics.jax.org/ Orthologous lncRNA annotation Sarropoulos et al., 2019 https://apps.kaessmannlab.org/lncRNA_app/ SNP database 90 Han Chinese genomes ftp://parrot.genomics.cn/gigadb/pub/10.5524/ 100001_101000/100302/90_Han_Chinese_ SNP_gatkvqsr_20170303.vcf.gz RNA binding proteins Zhu et al., 2019 http://lulab.life.tsinghua.edu.cn/postar/ GWAS Catalog NHGRI-EBI Catalog https://www.ebi.ac.uk/gwas/ PancanQTL Gong et al., 2018 http://bioinfo.life.hust.edu.cn/PancanQTL/ Experimental Models: Cell Lines Human: HEK293T cells ATCC Cat# CRL-3216, RRID: CVCL_0063 Human: HeLa cells ATCC Cat# CRM-CCL-2, RRID:CVCL_0030 (Continued on next page) e1 Molecular Cell 77, 1–15.e1–e6, February 6, 2020 .. Continued REAGENT or RESOURCE SOURCE IDENTIFIER Human: HT29 cells ATCC Cat# HTB-38, RRID:CVCL_0320 Human: GOS-3 cells DSMZ Cat# ACC-408, RRID:CVCL_2050 Human: K562 cells ATCC Cat# CCL-243, RRID:CVCL_0004 Human: U251 cells ECACC Cat# 09063001, RRID:CVCL_0021 Human: WPMY-1 cells ATCC Cat# CRL-2854, RRID:CVCL_3814 Human: U2OS cells ATCC Cat# HTB-96, RRID:CVCL_0042 Human: Jurkat cells ATCC Cat# TIB-152, RRID:CVCL_0367 Experimental Models: Organisms/Strains C57BL/6J Jackson Laboratory JAX: 000664 Oligonucleotides See Method Details for m6A-seq-qPCR based m6A level evaluation This paper N/A Software and Algorithms Trim_galore Babraham Institute http://www.bioinformatics.babraham.ac.uk/ projects/trim_galore/ TopHat2 v2.0.13 Kim et al., 2013 https://ccb.jhu.edu/software/tophat/ index.shtml samtools v1.7 Li, 2011 http://samtools.sourceforge.net/ MEME (Web-based) Bailey et al., 2009 http://meme-suite.org/tools/meme bedtools v2.27.1 Quinlan and Hall, 2010 https://bedtools.readthedocs.io/en/latest/ ANNOVAR Wang et al., 2010 http://annovar.openbioinformatics.org/en/ latest/ Homer v4.8 Heinz et al., 2010 http://homer.ucsd.edu/homer/ HISAT2 v2.1.0 Kim et al., 2015 https://ccb.jhu.edu/software/hisat2/index.shtml IGV v2.4.15 Thorvaldsdóttir et al., 2013 https://software.broadinstitute.org/software/igv/ Cufflinks v2.2.1 Trapnell et al., 2010 http://cole-trapnell-lab.github.io/cufflinks/ TissueEnrich Jain and Tuteja, 2019 https://tissueenrich.gdcb.iastate.edu Rtsne Seo and Lee, 2008 https://github.com/jkrijthe/Rtsne DOSE Yu et al., 2015 https://www.bioconductor.org/packages/ release/bioc/html/DOSE.html LDSC Bulik-Sullivan et al., 2015 https://github.com/bulik/ldsc

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

    ChIP-sequencing:

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

    Software:

    Article Title: DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts.
    Article Snippet: .. DNA methylation and histone H1 mediate transcriptional silencing of genes and transposable elements, but how they interact is unclear. ..

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