Name		Name	Last commit message	Last commit date
Latest commit History 7 Commits
Figure1_reporter_chip_nexus_captures_paused_polii		Figure1_reporter_chip_nexus_captures_paused_polii
Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing		Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing
Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing		Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing
Figure4A_S8_core_promoter_elements_and_paused_polii_halflives		Figure4A_S8_core_promoter_elements_and_paused_polii_halflives
Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing		Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing
Figure5_Inr_contributes_to_the_degree_of_Pol II_pausing		Figure5_Inr_contributes_to_the_degree_of_Pol II_pausing
Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters		Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters
Figure7A_S10_inr_variants_and_paused_polii_halflives		Figure7A_S10_inr_variants_and_paused_polii_halflives
Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing		Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing
FigureS12_expression_quantification		FigureS12_expression_quantification
FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters		FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters
FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing		FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing
FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a		FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a
FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability		FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability
pipeline		pipeline
rdata		rdata
shared_code		shared_code
Figure1_reporter_chip_nexus_captures_paused_polii.Rmd		Figure1_reporter_chip_nexus_captures_paused_polii.Rmd
Figure1_reporter_chip_nexus_captures_paused_polii.pdf		Figure1_reporter_chip_nexus_captures_paused_polii.pdf
Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing.Rmd		Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing.Rmd
Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing.pdf		Figure2_reporter_chip_nexus_recapitulates_endogenous_polii_pausing.pdf
Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing.Rmd		Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing.Rmd
Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing.pdf		Figure3_S7_changes_in_downstream_promoter_sequence_alter_polii_pausing.pdf
Figure4A_S8_core_promoter_elements_and_paused_polii_halflives.Rmd		Figure4A_S8_core_promoter_elements_and_paused_polii_halflives.Rmd
Figure4A_S8_core_promoter_elements_and_paused_polii_halflives.pdf		Figure4A_S8_core_promoter_elements_and_paused_polii_halflives.pdf
Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing.Rmd		Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing.Rmd
Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing.pdf		Figure4B_to_D_S9_tata_insertion_may_reduce_polii_pausing.pdf
Figure5_Inr_contributes_to_the_degree_of_Pol II_pausing.Rmd		Figure5_Inr_contributes_to_the_degree_of_Pol II_pausing.Rmd
Figure5_Inr_contributes_to_the_degree_of_Pol_II_pausing.pdf		Figure5_Inr_contributes_to_the_degree_of_Pol_II_pausing.pdf
Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters.Rmd		Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters.Rmd
Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters.pdf		Figure6_initiator_sequence_differs_between_tata_and_stably_paused_promoters.pdf
Figure7A_S10_inr_variants_and_paused_polii_halflives.Rmd		Figure7A_S10_inr_variants_and_paused_polii_halflives.Rmd
Figure7A_S10_inr_variants_and_paused_polii_halflives.pdf		Figure7A_S10_inr_variants_and_paused_polii_halflives.pdf
Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing.Rmd		Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing.Rmd
Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing.pdf		Figure7B_to_D_S11_inr_g_variant_plays_a_dominant_role_in_stabilizing_polii_pausing.pdf
FigureS12_expression_quantification.Rmd		FigureS12_expression_quantification.Rmd
FigureS12_expression_quantification.pdf		FigureS12_expression_quantification.pdf
FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters.Rmd		FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters.Rmd
FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters.pdf		FigureS3_paused_polii_stability_at_eight_drosophila_pseudoobscura_promoters.pdf
FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing.Rmd		FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing.Rmd
FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing.pdf		FigureS4_reporter_chipnexus_recapitulates_endogenous_polii_pausing.pdf
FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a.Rmd		FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a.Rmd
FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a.pdf		FigureS5_larger_promoter_region_required_for_recapitulating_polii_pausing_at_rpl13a.pdf
FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability.Rmd		FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability.Rmd
FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability.pdf		FigureS6_reporter_chipnexus_recapitulates_gene_specific_polii_pausing_stability.pdf
Inr_variant_halflife_wilcox_test_mutually_exclusive.csv		Inr_variant_halflife_wilcox_test_mutually_exclusive.csv
Inr_variant_halflife_wilcox_test_non_mutually_exclusive.csv		Inr_variant_halflife_wilcox_test_non_mutually_exclusive.csv
LICENSE		LICENSE
README.md		README.md
ami_setup_motes.md		ami_setup_motes.md
dps_genome_annotation.bed		dps_genome_annotation.bed
expression_quantification.csv		expression_quantification.csv
plasmid_annotation.bed		plasmid_annotation.bed
promoter_element_combination_halflife_wilcox_test_mutually_exclusive.csv		promoter_element_combination_halflife_wilcox_test_mutually_exclusive.csv
promoter_element_combination_halflife_wilcox_test_non_mutually_exclusive.csv		promoter_element_combination_halflife_wilcox_test_non_mutually_exclusive.csv
promoter_elements.txt		promoter_elements.txt
sample_summary.csv		sample_summary.csv

License

zeitlingerlab/Shao_eLife_2019

Folders and files

Latest commit

History

Repository files navigation

Shao reporter-chip-nexus paper

About

Resources

License

Stars

Watchers

Forks

Releases

Packages 0

Languages

Packages