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Additional file 7 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 7. Syntenic 1kb regions oocyte epigenetic profiling. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 8 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 8. Rat and mouse oocyte 1kb bin DNAme levels. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 9 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 9. Rat 10kb bins epigenetic profiling. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 2: Table S1. Data displayed in figure panels. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 3 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 3: Table S2. Rat and mouse differentially methylated regions. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 4 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 4: Table S3. Datasets generated and mined in this study. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 5 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 5. Allele specific RNAseq. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 6 of Conservation and divergence of canonical and non-canonical imprinting in murids
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Richard Albert, Julien; Kobayashi, Toshihiro; Inoue, Azusa; Monteagudo-Sánchez, Ana; Kumamoto, Soichiro; Takashima, Tomoya; Miura, Asuka; Oikawa, Mami; Miura, Fumihito; Takada, Shuji; Hirabayashi, Masumi; Korthauer, Keegan; Kurimoto, Kazuki; Greenberg, Maxim V. C.; Lorincz, Matthew; Kobayashi, Hisato — 2024 Additional file 6. Allele agnostic RNAseq. https://creativecommons.org/licenses/by/4.0/legalcode
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Additional file 2 of vmrseq: probabilistic modeling of single-cell methylation heterogeneity
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Shen, Ning; Korthauer, Keegan — 2024 Additional file 2: Table S1-S9. Table S1: Performance of clustering cells in Luo et al. [12] data with VMRs overlapped with targeted features. Default parameters, g = 100 and $$\theta = 0.7$$ θ = 0.7 , were used for calculation of the nearest neighbor score. The ‘broad classes’ refer to the 2 broad neuronal classesin Luo et al. [12] data, and ‘subtypes’ refer to 15 subtypes within those two classes. Gene promoters were defined as $$pm 2$$ p m 2 -kb windows around the transcription start sites of genes extracted from ENSEMBL version 80 [55]. Additional File 2: Table S9 lists data sources of the histone ChIP-seq annotation information. Table S2: Table with sample metadata from the mouse frontal cortex dataset. Table S3: Table with sample metadata from the multi-omic mouse gastrulation dataset. Table S4: Table with the correlation between gene expression and VMR/promoter methylation. Table S5: Table with the subtypes included in training parameters in transition probability and emission probability used as default in this study. Table S6: Table with the trained transition probability. Table S7: Table with the trained beta prior parameters of the emission probability for methylated grouping. Table S8: Table with the trained beta prior parameters of the emission probability for methylated grouping. Table S9: Table with data sources of histone ChIP-seq annotation information used in the experiments. https://creativecommons.org/licenses/by/4.0/legalcode

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