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


Saletore et al. Genome Biology 2012 13:175   doi:10.1186/gb-2012-13-10-175