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1_CAP_I_time_series_visualisation
2_CAP_I_bait_design
3_CAP_I_validation
5_CAP_I_RNAseq_atacR_markdown
6_CAP_I_GO_analysis_note
7_CAP_I_treatment_vs_treatment_note
8_CAP_I_pearson_correlation_note
README.md

README.md

Ding et al

Biorxiv: CAP-I

Repository structure

Each folder contains raw datasets, scripts, outputs.

Related Figures & Table

1_CAP_I_time_series_visualisation

  • Figure S1A/B, S3C
  • Table S2

2_CAP_I_bait_design

  • Figure 1A, S2A/B

3_CAP_I_validation

  • Figure 1B

5_CAP_I_RNAseq_atacR_markdown

  • Figure 2A, 3A, 4B/C/D, S3B, S4A/B/C/D/E
  • Table S3, S4, S5, S6

6_CAP_I_GO_analysis_note

  • Table S7

7_CAP_I_treatment_vs_treatment_note

  • Figure 4A

8_CAP_I_pearson_correlation_note

  • Figure 3C, Figure S3D

Figure & Table Details

Figures
Figure 1 CAP-I Bait Design and Validation
Figure 2 Reproducibility Test of RNA-CAP-I-seq
Figure 3 Quantification of RNA-CAP-I-seq
Figure 4 Correlation studies of RNA-CAP-I-seq from different genotypes and treatments
Supplementary Figures
Figure S1 Time-series expression of CAP-I genes under different conditions of immune activation
Figure S2 CAP-I bait design and RNA-CAP-I-seq experimental design
Figure S3 Overall quality assessment of RNA-CAP-I-seq data
Figure S4 Heatmaps of differential gene expression of mutants individually compared to wt
Supplementary Tables
Table S1 Information_of_ERGs_and_Control_Genes_in_CAP-I
Table S2 Time-series_Expression_of_CAP-I_genes
Table S3 Coverage_Information_of_CAP-I_gDNA_seq_Trial
Table S4 Read_Counts_of_RNA-CAP-I-seq_before_Normalisation
Table S5 Read_Counts_of_RNA-CAP-I-seq_post_Normalisation
Table S6 Log_Matrix_of_RNA-CAP-I-seq_Normalised_to_wt_un
Table S7 Geno_Ontology_Information_for_Clusters_in_Differential_Gene_Expression_Heatmap
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