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

Table 1 Comparison of MeRIP-seq and m⁶A-seq

	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

ISSN: 1474-760X