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
Differential enrichment analysis
4.1.1
H3K27me3
4.1.2
H3K27ac
4.1.3
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
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
7.1.1
H3K27me3
7.1.2
H3K27ac
7.1.3
H3K4me3
7.2
Block 2
7.2.1
H3K27me3
7.2.2
H3K27ac
7.2.3
H3K4me3
7.3
Logistic regressions
7.3.1
H3K27me3
7.3.2
H3K27ac
7.3.3
H3K4me3
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 length and recombination rates
Recombination rate
% intron
Published with bookdown
Appendix D: Parent-of-origin variation in transcription and chromatin regulation underly reproductive caste determination
Appendix D-8
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