Notes for high resolution methylation map link with transcriptome
 
1."Transcriptome" tracks
 
col:
signal: quantile normalization
sample: polyA RNA
tissue: whole plant tissue (aerial part)
plant: wild type, columbia
 
met1:
signal: quantile normalization
sample: polyA RNA
tissue: whole plant tissue (aerial part)
plant: met1 (METHYLTRANSFERASE1) mutant, columbia background
 
ddc:
signal: quantile normalization
sample: polyA RNA
tissue: whole plant tissue (aerial part)
plant: drm1 drm2 cmt3 (DOMAINS REARRANGED METHYLASE 1,2, and CHROMOMETHYLASE3) mutant, columbia background
 
2. "Methylome HMM" tracks
 
mCIP col/met1 BU:
signal: posterior probability of HMM by TileMap (significantly higher signal in wild type when the wild type methylated DNA is used as probe data compared to methylated DNA in met1 mutant.)
sample: enriched DNA by methyl cytosine antibody
tissue: whole plant tissue (aerial part)
plant: wild type and met1 mutant (columbia background)
 
mCIP met1/col BU:
signal: posterior probability of HMM by TileMap (significantly higher signal in met1 mutant when the mutant methylated DNA is used as probe data compared to wild type methylated DNA.)
sample: enriched DNA by methyl cytosine antibody
tissue: whole plant tissue (aerial part)
plant: met1 mutant and wild type
 
mCIP col/ddc BU:
signal: posterior probability of HMM by TileMap (significantly higher signal in wild type when the wild type methylated DNA is used as probe data compared to methylated DNA in ddc mutant)
sample: enriched DNA by methyl cytosine antibody
tissue: whole plant tissue (aerial part)
plant: wild type and ddc triple mutant (columbia background)
 
mCIP ddc/col BU:
signal: posterior probability of HMM by TileMap (significantly higher signal in ddc mutant when the mutant methylated DNA is used as probe data compared to wild type methylated DNA.)
sample: enriched DNA by methyl cytosine antibody
tissue: whole plant tissue (aerial part)
plant: ddc triple mutant and wild type
 
mCIP col BU/UB:
signal: posterior probability of HMM by TileMap (up in enriched DNA by methyl cytosine antibody )
sample: enriched DNA by methyl cytosine antibody and un-bounded DNA fraction by the antibody
tissue: whole plant tissue (aerial part)
plant: wild type (columbia)
 
mCIP met1 BU/UB:
signal: posterior probability of HMM by TileMap (up in enriched DNA by methyl cytosine antibody )
sample: enriched DNA by methyl cytosine antibody and un-bounded DNA fraction by the antibody
tissue: whole plant tissue (aerial part)
plant: met1 mutant (columbia background)
 
mCIP ddc BU/UB:
signal: posterior probability of HMM by TileMap (up in enriched DNA by methyl cytosine antibody )
sample: enriched DNA by methyl cytosine antibody and un-bounded DNA fraction by the antibody
tissue: whole plant tissue (aerial part)
plant: ddc triple mutant (columbia background)
 
HMBD col BU/UB:
signal: posterior probability of HMM by TileMap (up in enriched DNA by methylcytosine-binding domain of the human MeCP2 protein (MBD))
sample: enriched DNA by MBD and un-bounded DNA fraction by MBD
tissue: whole plant tissue (aerial part)
plant: wild type (columbia)
 
3. Details about TileMap with Hidden Markov Model: 
Reference: Ji, H. and Wong, W.H. 2005 Bioinformatics 21:3629 
Web site: http://biogibbs.stanford.edu/~jihk/TileMap/index.htm
 
4. link to accession:
Platform: [GPL1979], [GPL1980]
DNA methylation data: [GSE5094], [cel files]
Transcriptome data: [GSE5074], [cel files]

ncRNA sequences: [BT025666–BT025694]

 
5. link to original data list:
Data directory. 
 
6. Reference:
Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis
Xiaoyu Zhang, Junshi Yazaki, Ambika Sundaresan, Shawn Cokus, Simon W.-L.Chan, Huaming Chen, Ian R. Henderson, Paul Shinn, Matteo Pellegrini, Steve E. Jacobsen and Joseph R. Ecker