Table 1 |
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Comparison of MeRIP-seq and m6A-seq |
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|
MeRIP-seq [19] |
m6A-seq [20] |
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|
|
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|
Tissue/cell line |
C57BL/6 brain |
HEK293T |
HepG2 |
C57BL/6 liver |
|
|
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|
Organism |
Mouse |
Human |
Human |
Mouse |
|
|
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|
Replicates (n) |
3 |
1 |
||
|
|
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|
RNA preparation |
RiboMinus |
GenElute mRNA |
||
|
|
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|
IP antibody |
Synaptic Systems, NEB |
Synaptic Systems |
||
|
|
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|
IP rounds (n) |
2 |
1 |
||
|
|
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|
RNA fragment size |
100 bp |
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|
|
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|
RNA sequencing platform |
Illumina GAII and HiSeq2000 |
Illumina HiSeq2000 |
Illumina GAII |
|
|
|
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|
Sequenced control |
Yes |
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|
|
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|
Aligners |
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|
|
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|
Peak-finder |
Proprietary [20] |
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|
|
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|
Peak-finding algorithm |
Fisher's exact test of IP read enrichment |
Computed Winscore >2 (4 × enrichment) + filtering [20] |
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|
|
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|
Peaks reported (n) |
13,471 |
18,756 |
12,769 |
4,513 |
|
|
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|
Genes/transcripts reported |
4,654 genes |
5,768 genes |
7,240 transcripts |
3,442 transcripts |
|
|
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|
Peak enrichment |
Stop codon, internal exons |
Stop codon, TSS, internal exons, AS exons |
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|
|
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|
Saletore et al. Genome Biology 2012 13:175 doi:10.1186/gb-2012-13-10-175 |
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