{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Danio rerio"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14873"],"description":["Whole 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)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic 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."],"figure_sub":["MINSEQE Score","Assays and Data","Processed Data","organisation","MAGE-TAB Files"],"data_protocol":["Data 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)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["Bisulfite-seq"],"species":["Danio rerio"],"additional_accession":["ERP169517"],"pubmed_authors":["Ozren Bogdanovic","Thirsa Brethouwer"]},"is_claimable":false,"name":"Whole genome bisulfite sequencing from four stages of zebrafish sperm development","description":"Whole 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).","dates":{"release":"2025-06-09T00:00:00Z","modification":"2025-06-10T07:30:33.735Z","creation":"2025-02-25T11:34:18.078Z"},"accession":"E-MTAB-14873","cross_references":{"ENA":["ERP169517"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003753","EFO_0005518","EFO_0003816","EFO_0004184"]}}