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Table 1 Comparison of MeRIP-seq and m6A-seq

From: The birth of the Epitranscriptome: deciphering the function of RNA modifications

  MeRIP-seq [19] m6A-seq [20]
Tissue/cell line C57BL/6 brain HEK293T HepG2 C57BL/6 liver
Organism Mouse Human Human Mouse
Replicates (n) 3 1
RNA preparation RiboMinus GenElute mRNA
IP antibody Synaptic Systems, NEB Synaptic Systems
IP rounds (n) 2 1
RNA fragment size 100 bp
RNA sequencing platform Illumina GAII and HiSeq2000 Illumina HiSeq2000 Illumina GAII
Sequenced control Yes
Aligners BWA [38], TopHat [39] Novoalign [70], BowTie [71]
Peak-finder MeRIPPeR [19, 35] Proprietary [20]
Peak-finding algorithm Fisher's exact test of IP read enrichment Computed Winscore >2 (4 × enrichment) + filtering [20]
Peaks reported (n) 13,471 18,756 12,769 4,513
Genes/transcripts reported 4,654 genes 5,768 genes 7,240 transcripts 3,442 transcripts
Peak enrichment Stop codon, internal exons Stop codon, TSS, internal exons, AS exons