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Publicly Available Data Sets

Data Sets

 

Li Q, Eichten SR, Hermanson PJ, Springer NM. 2014. Inheritance patterns and stability of DNA methylation variation in maize near-isogenic lines. Genetics, 196(3): 667-676

GEO archive of B73-Mo17 near isogenic lines (NIL) leaf tissue meDIP-chip data: GSE51567

IGV formatted files for B73-Mo17 NIL meDIP-chip data

 

Eichten SR, Swanson-Wagner RA, Schnable J, Waters A, Hermanson P, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable P, Vaughn M, Springer NM. 2011. Heritable epigenetic variation among maize inbreds. PLoS Genet 7(11)

GEO archive of B73 and Mo17 leaf tissue meDIP-chip data: GSE29099

IGV formatted files for B73 and Mo17 leaf methylome data

 

Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh C, Xu W, Schnable P, Vaughn M, Gehring M, Springer NM. 2011. Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm. Plant Cell 7(1)

GEO archive of B73 and Mo17 endosperm tissue meDIP-chip data: GSE33730

IGV formatted files for B73 and Mo17 endosperm methylome data

SRA archive of RNAseq data for B73, Mo17, and reciprocal F1s: SRP009313

IGV formatted files for RNAseq genomic coverage from imprinting analysis

 

Eichten SR, Vaughn M, Hermanson P, Springer NM. 2012 Variation In DNA Methylation Patterns is More Common among Maize Inbreds than among Tissues. Plant Genome 10.3835

GEO archive of B73 and Mo17 tissues meDIP-chip data: GSE38503

IGV formatted files for B73 and Mo17 individual tissues and tissue contrast methylome data

SRA archive of RNAseq data for B73, Mo17, and reciprocal F1s: SRP013432

IGV formatted files for RNAseq genomic coverage from maize tissue analysis

 

Eichten SR, Ellis NA, Makarevitch I, Yeh C, Gent J, Guo L, McGinnis KM, Zhang X, Schnable PS, Vaughn MW, Dawe RK, Springer NM. 2012. Spreading of Heterochromatin is Limited to Specific Families of Maize Retrotransposons. PLoS Genet 8(12)

GEO archive of B73 and Mo17 leaf tissue meDIP-chip data: GSE29099

GEO archive of H3K9me2 chIP-chip data for B73, Mo17 and methylome data for mop1 mutant: GSE39460

IGV formatted files for B73, Mo17 zmet2 mutants, and mop1 mutant leaf methylome data

IGV formatted files for B73 and Mo17 H3K9me2 chIP-chip data

SRA archive of RNAseq data utilized: SRP013432(embryo, endosperm, ear) and SRP009313(leaf).

IGV formatted files for RNAseq genomic coverage from RTE spreading analysis

 
 
Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. Epigenetic and genetic influences on DNA methylation variation in maize populations. The Plant Cell (In Press).
 
GEO archive of meDIP-chip data on diverse inbred lines: GSE46949
 
SRA archive of RNAseq data: SRP018088
 
SRA archive of Whole genome bisulfite data: SRP022569
 
 
 
Array Platform Information

Maize 2.1M methylation array

GEO Platform: GPL13499

A NimbleGen 2.1M feature long oligo array was designed using B73 RefGen2 assembly, masked for repetitive sequences (J. Stein and D. Ware)  and then used to tile probes every 200bp (except  on chromosome 9 where we selected additional probes tiled every 56bp to improve resolution).  In addition, 35,000 control probes that match maize genomic DNA characteristics were selected to provide estimates of noise.

 

Maize 3x1.4M methylation array

GEO Platform: GPL15621

A NimbleGen 3x1.4M High-Density feature long oligo array was designed as a subset of uniquely mapping B73 probes from the Maize 2.1M methylation array. Coordinates are based on the B73 reference genome v2 physical positions (assembly RefGen_v2). Array was designed using probes initially found on the Maize 2.1M array platform (GPL13499). Probes were selected by being single-copy sequences within the maize RefGen_v2 masked genomic sequence. PROBE_ID values from this platform are conserved from their selections from GPL13499, allowing easy cross-comparison between experimental platforms.

 

Maize 12x270k DMR array

GEO Platform: GPL17181

A NimbleGen 12x270k High-Density feature long oligo array was designed to specifically assay over four thousand putative differentially methylated regions (DMRs) between a variety of diverse maize lines. This platform contains over 80,000 probes that were found on the previous two array platforms while also adding many new probes in the surrounding areas to obtain a probe spacing of ~50bp rather than 200bp. Control (non DMR) regions and technical replication of a subset of DMRs are also assayed on this platform.