Appendix D
About
1
WGS, mRNA-seq, and ChIP-seq
1.1
WGS
1.2
mRNA-seq
1.3
ChIP-seq
2
Transcriptomic Analyses
2.1
Differential gene expression analysis
2.2
WGCNA
3
Allele-Specific Transcriptomic Analyses
3.1
SNPs and transcripts
3.2
POE gene lists
3.3
192hpf WL & QL - allelic transcriptomics
3.3.1
Block 1
3.3.2
Block 2
3.4
24hpf eggs - allelic transcriptomics
3.4.1
Block 3
3.4.2
Block 4
4
ChIP-seq Analysis
4.1
Enrichment across promoters and gene bodies
4.2
Differential enrichment analysis
4.2.1
H3K27me3
4.2.2
H3K27ac
4.2.3
H3K4me3
5
Allele-Specific ChIP-seq Analyses
5.1
SNPs and peaks
5.2
POE peak lists
5.2.1
H3K27me3
5.2.2
H3K27ac
5.2.3
H3K4me3
5.3
H3K27me3
5.3.1
Gene bodies
5.3.2
Promoters
5.4
H3K27ac
5.4.1
Gene bodies
5.4.2
Promoters
5.5
H3K4me3
5.5.1
Gene bodies
5.5.2
Promoters
5.6
Combined results
5.6.1
Block 1
5.6.2
Block 2
6
HPTM-transcription dynamics
6.1
H3K27me3
6.1.1
Gene bodies
6.1.2
Promoters
6.2
H3K27ac
6.2.1
Gene bodies
6.2.2
Promoters
6.3
H3K4me3
6.3.1
Gene bodies
6.3.2
Promoters
7
POE HPTM enrichment-POE transcription dynamics
7.1
Block 1
H3K27me3
H3K27ac
H3K4me3
7.2
Block 2
H3K27me3
H3K27ac
H3K4me3
7.3
Logistic regression
H3K27me3 (gene body)
H3K27me3 (promoter)
H3K27ac (gene body)
H3K27ac (promoter)
H3K4me3 (gene body)
H3K4me3 (promoter)
8
GO enrichment analyses
8.1
DEGs & POE genes
8.2
WGCNA modules
8.3
HPTM differentially enriched regions
9
POE gene feature assessment
9.1
Spatial clustering
9.2
Intron feature analyses
Recombination rate
% intron
Intron GC
Intron CpG density
Published with bookdown
Supplementary Materials
S8
GO enrichment analyses
8.1
DEGs & POE genes
DEGs
192hpf larvae POE genes
192hpf larvae DE-POEs
24hpf egg POE genes
8.2
WGCNA modules
Module 2
Module 4
8.3
HPTM differentially enriched regions
H3K27me3
H3K27ac
H3K4me3