alexdemendoza/spongemethylation

SpongeMethylation

Files and code used for de Mendoza et al 2019 "Convergent evolution of a vertebrate-like methylome in a marine sponge". Nature Ecology and Evolution 2019 Oct;3(10):1464-1473. doi: 10.1038/s41559-019-0983-2

Free access to the manuscript: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31558833/.

Code

• Master_Script_deMendozaNEE.R

Files

• SequenceAlignments.zip: Amino acid sequence alignments of DNMT1, DNMT3, TET and UHRF1.
• Aqu2.1.genes.bed.gz: Amphimedon queenslandica Aqu2.1 gene annotation.
• Amphimedon_queenslandica.NNNNstrech.bed.gz: Regions encompassing Ns (gaps) in the Amphimedon genome assembly.
• bacterial_contigs: list of Amphimedon assembly contigs from bacterial origin.
• Amphimedon_UMR_LMR.zip: Output files from MethylSeekR UMR/LMR finding for each developmental sample.
• Amphimedon_DAPseq_TF_motifs.zip: Best motif as identified by HOMER2 for Amphimedon Transcription Factors DAP-seq/ampDAP-seq experiments.
• Amphimedon_DSS_DMRs.zip: Output files from DSS DMR calling across all developmental stages.
• CELSEQ_Aqu2.summarised.tsv.gz: Mean CEL-seq TPM summarised values for the developmental stages, from GSE70185.
• hmC_150windows_both_stages_01.bed.gz: Regions with hmCG/CG >= 0.1 in both Precompetent larva and juvenile stages.