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Project Plans ("roadmap") ("Age"-specific methylation,…
Project Plans ("roadmap")
Sex-linked methylation
Evaluate within-individual methylation differences (true test for X/Y-specific methylation) :pen:
Edit Daisy's phased X/Y rothschildianus reads :check:
Perform segregated mapping for each sample :pen:
Signals of methylation-mediated dosage compensation :world_map:
compare methylation in hemizygous X vs. XY vs. autosomal genes in males vs. females (plot 1:1) :check:
Expression-linked methylation
Correlate expression level (from RNA-seq data) to the methylation level of loci
Determine whether there's dosage compensation for X-linked loci in males
I think 1:1 plot of hemizygous genes in males and females should apply here?
"Age"-specific methylation
Extract the methylation data for the Y chromosome only from each karyotype and plot to look for general differences
Graph transcriptome-wide and genome-wide methylation levels :world_map:
Ideally, map the Y chromosome :pen:
Align Y sequences to the specific positions in each karyotype :pen:
Identify whether Y chromosome segments of different ages are differently methylated :pen:
Transposon-associated methylation
Shoddy initial attempt using transcriptome alignments :world_map:
Search for TEs in the "single-copy" genes?
Annotate genome
Map transcriptome (gene-ish?) to genome
Identify TE locations (in large contigs only?)
Visualise how (un)methyl C location is correlated with genes and TEs
Extract DNA methylation data for the large contigs with and without TEs (gene content relevant here?)
Compare TE content in Y chromosomes of different ages
Holistic (wrap-up)
Tie expression and methylation into one plot
Identify whether certain types of methylation are correlated with an increase/decrease in expression of certain loci
Determine how gene expression is affected by TE proximity?
Look for how substitutions (mutations) are correlated with age of Y chromosome and methylation state
Population Epigenetics?
Replication?