{"database": "metadata", "table": "run_metadata", "rows": [[38287, "SRR1616929", "SRX736533", "SRS724633", "SRP049069", "PRJNA264333", "A spinal opsin controls early neural activity and drives a behavioral light response", "GSE62527", "Transcriptome Analysis", "Purpose: using RNA seq as a screening tool to determine candidate genes of interest within a genetically defined neural subpopulation in the zebrafish embryonic spinal cord. Results: The early embryonic spinal cord displays patterns of spontaneous activity that generate the earliest motor behavior in the zebrafish. We show the behavior and the neural activity to be inhibited by environmental levels of light. Since at these young ages the fish is blind  and since restricted illumination patterns on the trunk of the fish can elicit a photo response  we hypothesized that the photo inhibition is an intrinsic property of the active central pattern generator network within the spinal cord. We FACS isolated cells from this network as well as those from a panneuronal population and sequenced mRNAs. Through differential expression analysis we identified vertebrate ancient long opsin a as a candidate and then further validated its function in the circuit through knockdown and rescue experiments. Overall design: RNA sequencing of 2 FACS purified neural populations from zebrafish spinal cord.", null, "pubmed:25484291", null, "HuC FP+", "GSM1528408", null, "tissue:spinal neurons|gal4 driver:HuC|population:panneuronal", "HuC FP+", "Illumina Casava1.8 software used for basecalling. Sequenced reads were mapped to Zv9 using Tophat v1.4.0 FPKMs were generated using Cufflinks v2.1.1 and compared using Cuffdiff Genome build: Zv9 Supplementary files format and content: tab delimited text file with FPKM for each sample", "spinal neurons", "Tails dissected free at the level of the 3rd somite and dissociated with trypsin/collagenase before FACS", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "20 hpf embryos were used", "gal4 driver:HuC|population:panneuronal", "GSM1528408", "GSM1528408: HuC FP+; Danio rerio; RNA Seq", "GSM1528408", null, "1", "Fluorescent neural cell bodies were FACS sorted into Trizol and flash frozen before total RNA extraction and polyA selection. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM1528408", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP049069", null, null, "HuCFP_R2.fastq HuCFP_R1.fastq", "fastq fastq", 5590606800.0, 27953034.0, "GSM1528408 r1", "0:100 1:100", "A:1550775239;C:1214652319;G:1269909429;T:1544634947;N:10634866", 100, 100, null, null, 1550775239, 1214652319, 1269909429, 1544634947, 10634866, "SRX736533", "SRS724633", "SRA192701", "GEO", "Isacoff, MCB, UC Berkeley", 2, 0.90003, 0.87337, 0.19389, 0.18827, 0.74594, 0.75041, 0.50589, 0.50314, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-10-20", "Segmentation", "Embryo", "Brain", "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": ["38287"], "units": {}, "query_ms": 8.986337998067029}