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Additional file 13: Table S6. Average DNA methylation results for different functional genomic elements

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Additional file 6: Table S3. Methylation evidence results for the uniquely aligned, de-duplicated and M-bias filtered reads

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Additional file 22: Figure S13. L1ORF1p expression in MPI of male germ cells. Temporal expression of L1ORF1p (green) was evaluated in testicular cryosections in the context of seminiferous epithelial cycle composed of stages I–XII. Haploid spermatids are identified based on numbers 1 through 16 according to degree of differentiation (only some are highlighted here). The basal membrane is outlined by the bright cross-reacting red staining. Following spermatogenic progression based on acrosome development marked by sp56 (red) and DNA stain, DAPI (blue), it is determined that cytoplasmic L1ORF1p is first seen in L/Z spermatocytes at stage XI (or X–XI) and persists from Z (stages XI–XII) to mid-P spermatocytes (stages I through VI–VII). L1ORF1p is not detectable in late P cells found stages VII–X, but is evident in the cytoplasm of elongating spermatids (see stages VII–IX) and is also detected as small dots in early round spermatids. The sp56 staining for spermatids beyond step 13 is difficult to see here, since the acrosome spreads very thin at this time. The selection inside the white box of the merged image (top row) is shown as a close-up inset in the DAPI-containing image row and represents a single confocal plane in an otherwise 3-D stacked image, highlighting the cytoplasmic distribution of L1ORF1p in meiotic prophase I spermatocytes. Bar = 10 micron

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Additional file 4: Table S1. Bisulfite sequencing, alignment and read de-duplication results summary

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Additional file 1: Figure S1. Schematic representation of main events in meiotic prophase I. Following premeiotic DNA replication in preleptonema (PL), parental homologous chromosomes (each containing two sister chromatids) develop chromosome axes (marked by SYCP3 protein), pair and synapse in leptonema (L) and zygonema (Z). Synapse is complete in pachynema (P) indicated by the complete overlap of SYCP3 and SYCP1 proteins. Following the completion of meiotic recombination, the synaptonemal complex disassembles in diplonema (D). Approximate duration of MPI substages are indicated (hrs). Figure adapted from [70]

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Additional file 8: Table S5. Coverage and methylation evidence for common CpGs (covered in common between samples of individual biological replicate groups)

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Additional file 9: Figure S4. CpG DNA methylation levels across chromosome length. DNA methylation was averaged using sliding non-overlapping windows of 100 kb

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Additional file 3: Figure S3. Transcript abundance of select genes in individual MPI germ cells using RNA-seq, expressed as RPKM. Prominent transcripts from (A) testicular somatic cells, including Sertoli, Leydig and Macrophage cells, were examined to assess the level of contamination and included Amh, Ccl2, Cd9, Cyp11a1, Cyp17a1, Fn1, Fshr, Gap43, Gata1, Gata4, Gpc3, Lhcgr, Lum, Mmp12, Mmp9, Pla2g4a, Rlf, Star, Tead2 and Vcam1. Meiosis-specific gene Mlh3 is used for relative comparison. Transcript abundance of genes associated with (B) differentiated (blue) and undifferentiated (beige) Spg, (C) meiosis-specific synaptonemal complex (SC) formation, (D) meiotic onset (Stra8), meiosis-specific sister chromatid cohesion complex (Smc1b, Rec8, Rad21l and Stag3), recognition of meiotically programmed DSBs (H2afx) and other early meiosis-associated genes (e.g., Mei1), (E–F) DSB formation and repair and recombination were evaluated. (G-H) Replication-dependent histone variant genes are highly expressed and enriched in PL spermatocytes. Twelve replication-dependent histone variant genes with high transcript abundance are shown. Selected are whose genes that are known to be highly enriched in early spermatocytes at 9-dpp testis, but not 2-dpp (gonocytes), 25-dpp (enriched in round spermatids) or 60-dpp (enriched in haploid cells). (I) Two genes, H3f3a and H3f3b, encoding replication-independent histone H3.3 were examined

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Additional file 15: Table S8. (A) Features of large differentially methylated blocks in germ cells. (B) Mean percentage (%) of genomic feature quantitation (covered by remethylating DMRs)

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Additional file 16: Figure S8. DNA methylation pattern in PL overlaps with replication timing, an example of chromosome 14, biological replicate one. (A) Plot of CpG DNA methylation of MPI stages, premeiotic Spg and post-meiotic Spz, across chromosome 14, which is ~ 125 Mbp long. Biological Replicate 1 is shown. (B) Replication timing (RT) data from CH12 cells (mouse B cell lymphoma) [71] and (C) genome sequencing coverage after WGBS-seq, viewed in SeqMonk program