{"database": "metadata", "table": "run_metadata", "rows": [[47716, "SRR6829411", "SRX3785500", "SRS3038464", "SRP135259", "PRJNA438111", "RNA seq analysis on zebrafish Notch 3 mutants and adult neural stem cells", "GSE111765", "Transcriptome Analysis", "The goal of this study is to identify the Notch3 targets directly responsible for maintaining the quiescent state and the stemness of adult pallial zebrafish Radial Glia. Overall design: Three independent experiments with 15 larval brains for each condition were performed for library construction from genotyped notch3 /  mutant versus notch3+/+ larvae  crossed into the gfap:gf. Three independent experiments with 20 adult telencephali were performed for library construction from her4:drfp;mcm5:gfp double transgenic fish.", null, "pubmed:29695612", null, "notch pos rep1", "GSM3039484", null, "source name:head  without xxx|tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia", "notch pos rep1", "basecalls performed using bcl2fastq2 v2.15.0 trimming off adaptors Sequenced reads were mapped to the Zv9 zebrafish genome using TopHat2 with following parameters tophat  segmentlength20  segment mismatches 1 p 4  o output.sam ref.fasta R1 001 egal.fastq R2 001.egal.fastq Genome build: Zv9 Supplementary files format and content: delimited text files include raw read counts.", "head  without xxx", null, "The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:head  without xxx|age:7days|genotype:WT|cell types:radial glia", "GSM3039484", "GSM3039484: notch pos rep1; Danio rerio; RNA Seq", "GSM3039484", null, "1", "The notch3fh332 line was crossed into the gfap:egfp transgenic background. The heads were dissected and cells dissociated  were FACS sorted from genotyped 7dpf larval heads. Brains were dissected and cells dissociated were FACS sorted from the pallium of double transgenic her4:drfp;mcm5:egfp adult fish  to recover RFP positive qRGs  RFP/GFP double positive aRGs and GFP positive aNPs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM3039484", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP135259", null, null, "pos-pos-17-04-mix1_S2_all_R1_001_egal.fastq.gz pos-pos-17-04-mix1_S2_all_R2_001_egal.fastq.gz", "fastq fastq", 10302973813.0, 52489402.0, "GSM3039484 r1", "0:98.14 1:98.15", "A:3331056733;C:1851923955;G:1872031048;T:3239709185;N:8252892", 98, 98, null, null, 3331056733, 1851923955, 1872031048, 3239709185, 8252892, "SRX3785500", "SRS3038464", "SRA666168", "GEO", "Zebrafish neurogenetics, Stem cell and development, Institut Pasteur Paris", 2, 0.88173, 0.88043, 0.36084, 0.35676, 0.70794, 0.70936, 0.49847, 0.4986, 100, 100, "B", "B", "biological fallback assumption", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "France", "2018-03-13", "Larval", "Larval", "Head", "Nervous 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": ["47716"], "units": {}, "query_ms": 10.210376000031829}