Scripts and notebooks related to the analysis and generation of figures for Guerreiro et al., 2024, Nature Genetics (in press).
The table below provides an overview indicating the notebook in which each figure was generated.
| Figure | Notebook |
|---|---|
| Figure 1a | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Figure 1b | 1_Preimplantation.structural_properties_of_LADs.part2d.single-cell_UMAPs.FR231030.ipynb |
| Figure 1c | FR231214.preimplantation_transcription.homozygous_untreated_main_analyses.Rmd |
| Figure 1d | 1_Preimplantation.structural_properties_of_LADs.part2c.metric_of_similarity.all_Lmnb1_conditions.FR231030.ipynb |
| Figure 1e | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Figure 1f | 1_Preimplantation.structural_properties_of_LADs.part2c.metric_of_similarity.all_Lmnb1_conditions.FR231030.ipynb |
| Figure 2a | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Figure 2b | 4_Preimplantation.other_constructs.part3.metric_of_similarity.different_constructs_at_2cell_stage.ipynb |
| Figure 2c | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 2d | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 2e | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Figure 2f | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 3a | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 3b | 6_Preimplantation.EED_mKO_experiments.part2.enirchment_over_H3K27me3_domains.FR231005.ipynb |
| Figure 3c | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 3d | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 3e | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 3f | 6_Preimplantation.EED_mKO_experiments.part6.effects_of_treatments_on_DamOnly_and_H3K9me3.ipynb |
| Figure 3g | 6_Preimplantation.EED_mKO_experiments.part6.effects_of_treatments_on_DamOnly_and_H3K9me3.ipynb |
| Figure 3h | NA |
| Figure 3i | microscopy.plotting_results.ipynb |
| Figure 3j | NA |
| Figure 4a | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Figure 4b | 6_Preimplantation.EED_mKO_experiments.part2.enirchment_over_H3K27me3_domains.FR231005.ipynb |
| Figure 4c | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Figure 4d | microscopy.plotting_results.ipynb |
| Figure 4e | microscopy.plotting_results.ipynb |
| Figure 4f | NA |
| Figure 5a | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Figure 5b | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Figure 5c | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Figure 5d | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Figure 5e | 1_Preimplantation.structural_properties_of_LADs.part2c.metric_of_similarity.all_Lmnb1_conditions.FR231030.ipynb |
| Figure 5f | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Figure 5g | 1_Preimplantation.structural_properties_of_LADs.part2b.similarities_between_cells.heterozygous.FR231030.ipynb |
| Extended Data Figure 1a | 0_Preimplantation.QC.part1.sample_filtering.FR231030.ipynb |
| Extended Data Figure 1b | 0_Preimplantation.QC.part1.sample_filtering.FR231030.ipynb |
| Extended Data Figure 1c | 0_Preimplantation.QC.part1.sample_filtering.FR231030.ipynb |
| Extended Data Figure 1d | 0_Preimplantation.QC.part1.sample_filtering.FR231030.ipynb |
| Extended Data Figure 1e | 0_Preimplantation.QC.part2.correlation_with_Borsos_and_NBT.FR231030.ipynb |
| Extended Data Figure 1f | 0_Preimplantation.QC.part2.correlation_with_Borsos_and_NBT.FR231030.ipynb |
| Extended Data Figure 1g | 1_Preimplantation.structural_properties_of_LADs.part7.Comparison_to_Payne2020.FR220203.ipynb |
| Extended Data Figure 1h | FR231214.preimplantation_transcription.homozygous_untreated_main_analyses.Rmd |
| Extended Data Figure 2a | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 2b | 1_Preimplantation.structural_properties_of_LADs.part2a.similarities_between_cells.homozygous.FR231030.ipynb |
| Extended Data Figure 2c | 1_Preimplantation.structural_properties_of_LADs.part2c.metric_of_similarity.all_Lmnb1_conditions.FR231030.ipynb |
| Extended Data Figure 2d | 1_Preimplantation.structural_properties_of_LADs.part3b.NL_association_of_chromosome_extremities.all_conditions.FR231030.ipynb |
| Extended Data Figure 2e | 1_Preimplantation.structural_properties_of_LADs.part3b.NL_association_of_chromosome_extremities.all_conditions.FR231030.ipynb |
| Extended Data Figure 3a | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 3b | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 3c | 1_Preimplantation.structural_properties_of_LADs.part2d.single-cell_UMAPs.FR231030.ipynb |
| Extended Data Figure 3d | 1_Preimplantation.structural_properties_of_LADs.part1b.LAD_size_and_coverage.heterozygous.FR231030.ipynb |
| Extended Data Figure 3e | 1_Preimplantation.structural_properties_of_LADs.part3b.NL_association_of_chromosome_extremities.all_conditions.FR231030.ipynb |
| Extended Data Figure 3f | 1_Preimplantation.structural_properties_of_LADs.part3b.NL_association_of_chromosome_extremities.all_conditions.FR231030.ipynb |
| Extended Data Figure 4a | 3_Preimplantation.Relating_NLassociation_and_transcription.part2a.relating_variability_in_NL_and_transcription.FR220912.ipynb |
| Extended Data Figure 4b | 4_Preimplantation.other_constructs.part3.metric_of_similarity.different_constructs_at_2cell_stage.ipynb |
| Extended Data Figure 4c | 4_Preimplantation.other_constructs.part1.comparison_to_ChIPseq_10kb.FR220928.ipynb |
| Extended Data Figure 4d | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 4e | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Extended Data Figure 4f | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Extended Data Figure 4g | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Extended Data Figure 4h | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Extended Data Figure 5a | microscopy.plotting_results.ipynb |
| Extended Data Figure 5b | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 5c | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 5d | 5.2_Preimplantation.simplified_bin_clustering.part2.visualizing_clustered_heatmaps.FR231006.ipynb |
| Extended Data Figure 5e | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 5f | 6_Preimplantation.EED_mKO_experiments.part6.effects_of_treatments_on_DamOnly_and_H3K9me3.ipynb |
| Extended Data Figure 6a | 1_Preimplantation.structural_properties_of_LADs.part0.example_tracks.FR231030.ipynb |
| Extended Data Figure 6b | 6_Preimplantation.EED_mKO_experiments.part6.effects_of_treatments_on_DamOnly_and_H3K9me3.ipynb |
| Extended Data Figure 6c | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 6d | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 6e | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 6f | 6_Preimplantation.EED_mKO_experiments.part1.initial_comparison_insilico_populations.FR231108.ipynb |
| Extended Data Figure 6g | microscopy.plotting_results.ipynb |
| Extended Data Figure 6h | microscopy.plotting_results.ipynb |
| Extended Data Figure 6i | 2_Preimplantation.LAD_coordination.part2b.coordination_of_PADs.ipynb |
| Extended Data Figure 6j | 2_Preimplantation.LAD_coordination.part2b.coordination_of_PADs.ipynb |
| Extended Data Figure 6k | 6_Preimplantation.EED_mKO_experiments.part9.Viability_assay_plot.ipynb |
| Extended Data Figure 6l | FR231204.Cbx7-Lap2b_experiment.viability_blastocyst_expression_analysis.Rmd |
| Extended Data Figure 7a | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Extended Data Figure 7b | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Extended Data Figure 7c | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Extended Data Figure 7d | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Extended Data Figure 7e | 6_Preimplantation.EED_mKO_experiments.part7.NL_association_based_on_NL_affinity_and_H3K27me3_levels.ipynb |
| Extended Data Figure 7f | 1_Preimplantation.structural_properties_of_LADs.part1b.LAD_size_and_coverage.heterozygous.FR231030.ipynb |
| Clustering genomic bins | 5.2_Preimplantation.simplified_bin_clustering.part1.Performing_clustering.ipynb |