{"database": "metadata", "table": "run_metadata", "rows": [[49077, "SRR7641832", "SRX4505262", "SRS3625654", "SRP156282", "PRJNA484346", "Epigenetic regulation of zebrafish intestinal development", "GSE118076", "Other", "The goal of the experiment was to characterize the wild type larval intestine in zebrafish. Tgcldn15la:GFP intestine specific transgene was used to ease dissections. RNAseq was performed at 5  7  9 dpf on wild type dissected intestines to characterize the transcriptome. ChIPseq was performed at 5  7  9 dpf on wild type dissected intestines to check the intestinal presence of active H3K4me3 and repressive H3K27me3 chromatin marks and to correlate their presence with intestinal gene expression. Overall design: RNAseq of wild type dissected Danio rerio intestines  pools of 10 intestines in triplicates at 5  7  and 9 dpf. ChIPseq of wild type dissected Danio rerio intestines  pools of 25 intesines +5 set aside for input DNA in duplicates at 5  7  and 9 dpf for H3K4me3 and H3K27me3.", null, null, null, "Danio rerio RNAseq intestine 5dpf wt2", "GSM3318280", null, "source name:intestine|strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "Danio rerio RNAseq intestine 5dpf wt2", "RNA seq reads from dissected intestines were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Normalized counts obtained with DESeq2 version 1.16.1 ChIPseq reads from dissected intestines were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "intestine", null, "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "Zebrafish Danio rerio were housed under standard conditions in a 14:10 light/dark cycle. Embryo clutches were spawned from pairs of adults separated overnight from the batch  reared in E3 medium at 28.5\u00b0C and staged following Kimmel et al 1995. Larvae were fed a standard Gemma Micro 75 Skretting USA diet  supplemented with rotifer Brachionus spp. polyculture and Artemia according to guidelines.", "strain:AB|tissue:intestine|age:5 dpf|genotype:wild type  tgcldn15la:GFP|chip antibody:n/a", "GSM3318280", "GSM3318280: Danio rerio RNAseq intestine 5dpf wt2; Danio rerio; RNA Seq", "GSM3318280", null, "1", "Dissected intestines were lyzed in Trizol and total RNA was extracted  followed by in column ZYMO RNA microprep Dnase treatment. Total RNA from dissected intesines was depleted of ribosomal RNA RiboZero. post RNA fragmentation and cDNA synthesis  standard Illumina KAPA HYPERprep library preparations were made.", "GEO Accession:GSM3318280", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP156282", null, null, "lane1_BSwt5dpf2_GCCAAT_R2.fastq.gz lane1_BSwt5dpf2_GCCAAT_R1.fastq.gz", "fastq fastq", 2424100404.0, 28187214.0, "GSM3318280 r1", "0:43 1:43", "A:657799034;C:534330605;G:575770800;T:655604713;N:595252", 43, 43, null, null, 657799034, 534330605, 575770800, 655604713, 595252, "SRX4505262", "SRS3625654", "SRA751578", "GEO", "Molecular Biology, Radboud University", 2, 0.85487, 0.83514, 0.56287, 0.53286, 0.69583, 0.69658, 0.54518, 0.55246, 43, 43, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "bulk", "unknown", "unknown", null, "Netherlands", "2018-08-03", "Larval", "Larval", "Gut", "Digestive 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": ["49077"], "units": {}, "query_ms": 10.615743000016664}