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SRX14011277: GSM5852927: SL_1_L; Folivora; Bisulfite-Seq
1 ILLUMINA (Illumina HiSeq 3000) run: 21.4M spots, 1.1G bases, 429.9Mb downloads

Submitted by: NCBI (GEO)
Study: Comparative analysis of genome-scale, base-resolution DNA methylation profiles across 580 animal species
show Abstracthide Abstract
We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive dataset defined a “genomic code” of DNA methylation, which allowed us to predict global and locus-specific DNA methylation from the DNA sequence within and across species. This code appears broadly conserved throughout vertebrate evolution, with two major transitions – once in the first vertebrates and again with the emergence of reptiles. Beyond the central role of species-specific DNA sequence composition, our dataset identified the tissue type and the individual as two main sources of DNA methylation variability within species. Tissue type was the dominant factor in fish, birds, and mammals, while in invertebrates, reptiles, and amphibians both factors were similarly strong. Cross-species comparisons focusing on heart and liver tissues supported a highly conserved role of DNA methylation for tissue type and identity and cross-mapping based promoter methylation analysis revealed divergence at specific genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution. Overall design: Dataset comprises 2443 DNA methylation profiles (RRBS) covering 580 animal species (535 vertebrates and 45 invertebrates) and more than 10 major tissue types with a foucs on heart and liver, analysed in a reference-free manner.
Sample: SL_1_L
SAMN25560678 • SRS11849098 • All experiments • All runs
Organism: Folivora
Library:
Instrument: Illumina HiSeq 3000
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: Reduced Representation
Layout: SINGLE
Construction protocol: Reduced representation bisulfite sequencing (RRBS) was performed as described in Klughammer et al., Cell Reports 2015, using 100 ng of genomic DNA for most samples, while occasionally going down to 1 ng for samples with low DNA amounts (Supplementary Table 1). To assess the bisulfite conversion efficiency independent of CpG context, methylated and unmethylated spike-in controls were added at a concentration of 0.1%. For most samples, DNA was digested using the restriction enzymes MspI and TaqI in combination (as opposed to only MspI in the original protocol) in order to increase genome-wide coverage. For certain older samples, only MspI was used Restriction enzyme digestion was followed by fragment end repair, A-tailing, and adapter ligation. Fi-nally, the libraries were size selected by performing a 0.75× cleanup with AMPure XP beads (Beckman Coulter, A63881) retaining fragments of about 100 bp to 1000 bp length. The amount of effective li-brary was determined by qPCR, and samples were multiplexed in pools of 10 with similar qPCR Ct values. The pools were then subjected to bisulfite conversion, followed by library enrichment with PCR. Enrichment cycles were determined using qPCR and ranged from 6 to 18 (median: 11). After con-firming adequate fragment size distributions on Bioanalyzer High Sensitivity DNA chips (Agilent),
Experiment attributes:
GEO Accession: GSM5852927
Links:
Runs: 1 run, 21.4M spots, 1.1G bases, 429.9Mb
Run# of Spots# of BasesSizePublished
SRR1785052721,363,0721.1G429.9Mb2022-06-19

ID:
19707978

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