biostudies-arrayexpressDanio reriohttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14873Whole genome bisulfite sequencing of four stages of FACS sorted zebrafish male germ cells, isolated from adult testes (spermatogonia, spermatocytes I, round spermatids and mature sperm).biostudies-arrayexpressNucleic Acid Extraction - Samples were dissolved in homogenization buffer (20 mM Tris pH 8.0, 100 mM NaCl, 15 mM EDTA, 1% SDS, 0.5 mg/ml Proteinase K) at 55⁰C. Two Phenol/Chlorophorm/Isoamylalcohol (25:24:1, PCI) extractions were performed. DNA was precipitated using 1/5 volume of 4 M NH4Ac and 2.5 volumes of ice-cold absolute ethanol, and 1uL of linear acrylamide. Samples were incubated overnight at -20⁰C. The DNA was pelleted and resuspended in nuclease free water.Library Construction - Bisulfite converted libraries were generated using the Pico Methyl-Seq Library Prep Kit (Zymo Research, Cat. D5456) following manufacturer’s instructions.Sequencing - Libraries were sequenced on the Illumina NovaSeq X Plus Series platform (150 PE).Sample Collection - A pool of fresh testicular samples was dissected and disaggregated by a combination of mechanical and enzymatic methods. The resulting individualized cells were fixed in formaldehyde and then, sorted using a BD FACSDiscover S8 Cell Sorter. Cells were sorted according to their morphology, nucleus complexity and DNA content. Four different populations were sorted: spermatogonia, primary spermatocytes, round spermatids and sperm.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Files were trimmed using Trimmomatic (HEADCROP:5 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50) and mapped using Bismark (--non_directional --local -X 2000). Methylation was called using MethylDackel(--mergeContext --minOppositeDepth 10 --maxVariantFrac 0.5). DMRs were detected using DSS (delta=0.2, p.threshold=0.05, minlen=100, minCG=10, dis.merge=100).UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XBisulfite-seqDanio rerioERP169517Ozren BogdanovicThirsa BrethouwerfalseWhole genome bisulfite sequencing from four stages of zebrafish sperm developmentWhole genome bisulfite sequencing of four stages of FACS sorted zebrafish male germ cells, isolated from adult testes (spermatogonia, spermatocytes I, round spermatids and mature sperm).2025-06-09T00:00:00Z2025-06-10T07:30:33.735Z2025-02-25T11:34:18.078ZE-MTAB-14873ERP169517EFO_0002944EFO_0004170EFO_0003753EFO_0005518EFO_0003816EFO_0004184