DOI: 10.5061/dryad.hs200
title: Data from: EpiRADseq: scalable analysis of genome-wide patterns of methylation using next-generation sequencing

description: 1. Research addressing the role of epigenetics in a diversity of
 experimental and natural systems is rapidly accumulating. Diverse methods
 have been developed to study epigenetic states, including bisulfite
 sequencing and AFLP-based approaches. However, existing methods are
 sometimes difficult to apply to non-traditional model organisms that lack
 genomic resources (bisulfite sequencing), and can fail to be economical
 and readily scalable to diverse research questions because of reliance on
 traditional Sanger sequencing (AFLP approaches). 2. Here we develop a
 reduced-representation library-based approach that is scalable and
 economical to quantitatively compare patterns of genome-wide methylation.
 This approach shares substantial similarity to the now widely used double
 digest restriction-site associated DNA sequencing-based method (ddRADseq),
 except that it utilizes a methylation-sensitive restriction enzyme. This
 method therefore identifies changes in the genomic methylation state of
 cytosine (to 5-methyl-cytosine; 5mC) by sampling loci (via next-generation
 sequencing) that are not methylated within a sample. We test this method
 to identify shifts in the epigenome of clonal water fleas (Daphnia
 ambigua) in response to exposure to fish predator cues, which are known to
 induce transgenerational changes in life history traits. 3. We found
 evidence for differential transgenerational responses (inferred via
 significant shifts in the methylation state of sampled loci) to predator
 cues among our treatment groups, and remarkably consistent responses
 within treatment groups. Our results demonstrate that this method is
 capable of producing highly repeatable results even without the use of a
 reference genome. 4. Applications of this general method are broad and
 diverse, and include the analysis of epigenetic shifts in both
 experimental and natural study systems.
description: Daphnia ambigua
 epiRADseq Pseudo-reference GenomeThe pseudo-reference
 genome was constructed using all epiRAD reads, which was used for read
 mapping and inferring methylation. This file is in fasta format and is
 compressed.Daphnia_ambigua_EpiRADseq_Reference.fasta.bz2Daphnia ambigua epiRADseq Mapping Output FilesA zipped archive containing BAM mapping files for each sample (3 replicates across 2 treatments) mapped to the Daphnia ambigua pseudo-reference genome.Daphnia_ambigua_EpiRADseq_Mapping_Files.tar.bz2Daphnia ambigua EpiRADseq Raw Count TablesA zipped archive containing the raw counts for each sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.Daphnia_ambigua_EpiRADseq_Raw_Counts.tar.bz2Daphnia ambigua P treatment - first generation with predatory cues treatment (3 replicates) - Raw Illumina ReadsA zipped fastq file that contains multiplexed reads from the three replicates from the predator treatment (generation 1). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the P treatments in the manuscript and with all applicable Dryad file names and processing steps.P_Gen1_Predator_Treatment.fastq.bz2Daphnia ambigua PN treatment - second generation without predatory cues treatment (3 replicates) - Raw Illumina ReadsA zipped fastq file that contains multiplexed reads from the three replicates from the no predator treatment (generation 2). A script within the Data_processing_scripts.tar.bz archive will automatically perform the parsing using a barcodes file located in that same archive. These replicates are referred to as the PN treatments in the manuscript and with all applicable Dryad file names and processing steps.PN_Gen2_NoPredator_Treatment.fastq.bz2Frequency summary of Daphnia pulex genome double digestA summary file that provides the number of fragments in given fragment size range. Based on an in silico digestion of the Daphnia pulex genome. The Perl script used to generate this data is contained with all other data processing scripts.Daphnia_pulex_summary_doubleDigest_CTGCAG_CCGG.txtDaphnia ambigua EpiRADseq Data Analysis Scripts, Files, & DocumentationA zipped archive containing all scripts necessary to quality-trim raw reads, construct the pseudo-reference genome, and map the reads back to the psuedo-reference to infer methylation. Each script contains a proper description of function and usage and the complete pipeline (from raw reads to counts) is automated and documented in the EpiRADseq_analysis.sh script.Data_processing_scripts.tar.bz2Daphnia ambigua EpiRADseq Rarefaction Raw Read FilesA zipped archive containing randomly subsetted read files from all replicates, which were used for rarefaction analysis.Rarefaction_Daphnia_ambigua_EpiRADseq_Raw_Reads.tar.bz2Daphnia ambigua EpiRADseq Rarefaction Mapping FilesA zipped archive containing BAM mapping files for each rarefacted sample (3 replicates across 2 treatments) mapped to the Daphnia ambigua pseudo-reference genome.Rarefaction_Daphnia_ambigua_EpiRADseq_Mapping_Files.tar.bz2Daphnia ambigua EpiRADseq Rarefaction Raw Count TablesA zipped archive containing the raw counts for each rarefacted sample (3 replicates across 2 treatments) derived from the mapping to the Daphnia ambigua pseudo-reference genome. The four columns (in order) are: (1) The reference sequence/contig ID, (2) The length of the sequence/contig, (3) The number of reads that mapped to the sequence/contig, and (4) the number of reads that didn't map to the sequence/contig.Rarefaction_Daphnia_ambigua_EpiRADseq_Raw_Counts.tar.bz2