{"database": "metadata", "table": "run_metadata", "rows": [[41848, "SRR5892568", "SRX3058261", "SRS2404197", "SRP100178", "PRJNA375788", "'Placeholder' nucleosomes underlie germline to embryo DNA methylation reprogramming [RNA Seq]", "GSE95031", "Transcriptome Analysis", "The function and retention/reprogramming of epigenetic marks during the germline to embryo transition is a key issue in developmental and cellular biology  with relevance to stem cell programming and trans generational inheritance.  In zebrafish  DNAme patterns are programmed in transcriptionally quiescent early cleavage embryos; paternally inherited patterns are maintained  whereas maternal patterns are reprogrammed to match the paternal pattern. Here we show that a 'placeholder' nucleosome  containing the histone H2A variant H2A.ZFV and H3K4me1  occupies virtually all regions lacking DNAme in both sperm and cleavage embryos \u2013 residing at promoters encoding housekeeping and early embryonic transcription factors.  Upon genome wide transcriptional onset  genes with the Placeholder become either active H3K4me3 marked or silent H3K4me3/K27me3 marked bivalent.  Importantly  functional perturbation causing Placeholder loss confers DNAme acquisition  whereas acquisition/expansion of Placeholder confers DNA hypomethylation and improper gene activation.  Thus  during transcriptionally quiescent stages gamete zygote cleavage  an H2A.ZFV/H3K4me1 containing Placeholder nucleosome deters DNAme  poising parental genes for either gene specific activation or facultative repression. Overall design: Transcript abundance was analyzed for zebrafish sperm  and cleavage stage embryos that were either wild type or mutant for the anp32e gene.", "parent bioproject:PRJNA375781", "pubmed:29456083", null, "Anp32e Null Sperm RNA Seq Rep1", "GSM2730571", null, "tissue:Sperm Stage|developmental stage:Sperm Stage|strain:NA|injection:NA|mutation:Anp32e Null", "Anp32e Null Sperm RNA Seq Rep1", "Reads were aligned to the Zv10 genome using Novoalign v2.8  Novocraft using the following options:  o SAM  r All 50 Sam files were then combined due to high correlation between technical and biological replicates. The Useq Pipeline was utilized   Sam parsed using the SAMTranscriptomeParser  followed by DefinedRegionDifferentialSeq which utilizes DeSeq2 to generate differential gene expression tables and FPKM values. Genome build: Zv10 Supplementary files format and content: RNASeq geneCount minimum10.xlsx: Excel file contains gene count table.", "Sperm Stage", null, "Embryos were lysed using Trizol with the addition of 2% SDS  then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold", null, "developmental stage:Sperm Stage|strain:NA|injection:NA|mutation:Anp32e Null", "GSM2730571", "GSM2730571: Anp32e Null Sperm RNA Seq Rep1; Danio rerio; RNA Seq", "GSM2730571", null, "1", "Embryos were lysed using Trizol with the addition of 2% SDS  then homogenized using a 20G needle. Sample were then phenol extracted and the aqueous phase was added to a Qiagen RNA miniElute column for final purification. Illumina TruSeq Stranded RNA kit with Rib Zero Gold", "GEO Accession:GSM2730571", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP100178", null, null, "Anp32e_Null_Sperm_RNA-Seq_Rep1.fastq.gz", "fastq", 3162821050.0, 63256421.0, "GSM2730571 r1", "0:50", "A:756571256;C:759039692;G:777010061;T:870095540;N:104501", 50, null, null, null, 756571256, 759039692, 777010061, 870095540, 104501, "SRX3058261", "SRS2404197", "SRA538756", "GEO", "Huntsman Cancer Institute", 1, 0.91819, null, 0.04312, null, 0.76307, null, 0.45972, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2017-08-03", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["41848"], "units": {}, "query_ms": 9.317645002738573}