{"database": "metadata", "table": "run_metadata", "rows": [[10153, "ERR5005141", "ERX4814424", "ERS5474661", "ERP125923", "PRJEB42059", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E-MTAB-9924", "Other", "DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes  however  non CG methylation mCH is also detectable in vertebrate tissues  most notably in the nervous system. In mammalian brains  it is well established that: i mCH is targeted to CAC trinucleotides by DNMT3A  ii enriched in gene bodies and repetitive elements  and iii associated with transcriptional repression. However  the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study  we analyse the transcriptomes RNA seq and methylome RRBS of developing zebrafish larvae 1 6 weeks and adult brain 6 month. We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 wpf brains", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", null, "Protocols: Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "3wpf rep2 RNA", "SAMEA7727288", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,", "ENA first public:2020 12 18|ENA last update:2020 12 17|External Id:SAMEA7727288|INSDC center alias:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC center name:Genomics and Epigenetics Division  Garvan Institute of Medical Research |INSDC first public:2020 12 18T17:06:48Z|INSDC last update:2020 12 17T08:36:39Z|INSDC status:public|Submitter Id:E MTAB 9924:3wpf rep2 RNA|age:3|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:5|organism part:brain|sample name:E MTAB 9924:3wpf rep2 RNA|sex:mixed|strain:Mixed AB and Tubingen", null, null, null, null, null, null, null, null, "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "E MTAB 9924:3wpf rep2 RNA p", "3wpf rep2 RNA p", "RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "Whole brains were dissected from zebrafish larvae and adults before being snap frozen in liquid nitrogen and stored at  80\u00b0C Genomic DNA gDNA was extracted from brains using the QIAGEN DNeasy Blood & Tissue Kit QIAGEN  Chadstone  VIC  Australia according to manufacturer instructions. For RNA extraction  half the lysate from the first step of the DNA extraction from the QIAGEN DNeasy Blood & Tissue Kit was added to TRIsure Bioline and purified following manufacturer instructions. All experiments in this study were performed in biological replicates. RNA seq libraries were prepared with 1000ng of input RNA material using the KAPA mRNA HyperPrep Kit  according to the manufacturer's instructions.", "Experimental Factor: age:3|Experimental Factor: genotype:wild type genotype|Experimental Factor: protocol:RNA Seq", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "ERP125923", "HiSeq X Ten paired end sequencing; RNA seq and RRBS of developing zebrafish larval brain and WGBS of 4 wpf WT and dnmt3aa/dnmt3ab CRISPR/CAS9 KO brain", "ENA FIRST PUBLIC:2020 12 18|ENA LAST UPDATE:2020 12 17", "3wpf_rep2_RNA_R1.fastq.gz 3wpf_rep2_RNA_R2.fastq.gz", "fastq fastq", 22804042203.0, 76957632.0, "E MTAB 9924:3wpf rep2 RNA R", "0:148.34 1:147.98", "A:6255991654;C:5120232312;G:5136799470;T:6288581486;N:2437281", 148, 147, null, null, 6255991654, 5120232312, 5136799470, 6288581486, 2437281, "ERX4814424", "ERS5474661", "ERA3199751", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", "Genomics and Epigenetics Division, Garvan Institute of Medical Research,|European Nucleotide Archive", 2, 0.93211, 0.93322, 0.20907, 0.2056, 0.6983, 0.71652, 0.53448, 0.5352, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-12-17", "Larval", "Larval", "Multi-tissue", "Multi-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": ["10153"], "units": {}, "query_ms": 11.382122998838895}