Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Choi JY, Purugganan MD

Date Published: November 14, 2017

DOI: https://doi.org/10.5061/dryad.1q778

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Title indica reference japonica query genome alignment result in BED format
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Description BED format genome alignment results where indica 93-11 was used as reference and japonica nipponbare genome was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.
Download Osat_indica_9311_REF-Osat_japonica_NPB_QU...ed.bed (1.968 Mb)
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Title japonica reference indica query genome alignment result in BED format
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Description BED format genome alignment results where japonica nipponbare was used as reference and indica 93-11 was used as query genome. Indica chromosome was named as SAI.chromosome_number and japonica chromosome named as SAJ.chromosome_number.
Download Osat_japonica_NPB_REF-Osat_indica_9311_QU...ed.bed (2.022 Mb)
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Title japonica genome LTR-RT and nearby host gene and the host genes' expression values
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Download japonica_transcript.txt (873.1 Kb)
Download README.txt (1.259 Kb)
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Title indica genome LTR-RT and nearby host gene and the host genes' expression values
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Download indica_transcript.txt (605.5 Kb)
Download README.txt (1.259 Kb)
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Title japonica genome LTR-RT methylation levels
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Download japonica_methyl.txt (993.6 Kb)
Download README.txt (2.292 Kb)
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Title indica genome LTR-RT methylation levels
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Download indica_methyl.txt (1.045 Mb)
Download README.txt (2.292 Kb)
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Title japonica genome LTR-RT up and downstream region methylation levels
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Download japonica_methyl_updown.txt (21.35 Mb)
Download README.txt (2.386 Kb)
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Title indica genome LTR-RT up and downstream region methylation levels
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Download indica_methyl_updown.txt (30.71 Mb)
Download README.txt (2.386 Kb)
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Title Methylation level for LTR-RT and its up or downstream region in japonica genome and its orthologous region in indica
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Download japonica_methyl_updown_ortholog.txt (18.79 Mb)
Download README.txt (3.108 Kb)
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Title Methylation level for LTR-RT and its up or downstream region in indica genome and its orthologous region in japonica
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Download indica_methyl_updown_ortholog.txt (17.18 Mb)
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When using this data, please cite the original publication:

Choi JY, Purugganan MD (2017) Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice. Molecular Biology and Evolution, online in advance of print. https://doi.org/10.1093/molbev/msx284

Additionally, please cite the Dryad data package:

Choi JY, Purugganan MD (2017) Data from: Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice. Dryad Digital Repository. https://doi.org/10.5061/dryad.1q778
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