{"database": "metadata", "table": "run_metadata", "rows": [[36573, "SRR592703", "SRX195410", "SRS369337", "SRP016132", "PRJNA177642", "Danio rerio Transcriptome or Gene expression", "PRJNA177642", "Other", "Pineal glands of adult zebrafish were sampled every 4 hours for 48 hours.", null, null, "Adult 0.5 1.5 years old transgenic zebrafish Tgaanat2:EGFPY8 which express enhanced green fluorescent protein EGFP in the pineal gland under the control of the aanat2 regulatory regions were used. Fish were raised under 12 hr light:12 hr dark LD cycles in a temperature controlled room and transferred to constant darkness DD for tissue collection. Fish were anesthetized in 1.5 mM Tricane Sigma sacrificed by decapitation and pineal glands were removed under a fluorescent dissecting microscope. Starting from circadian time CT 14 pineal glands were collected at 4 hr intervals for 48 hours 12 time points identified as CT 14 18 22 2 6 10 14b 18b 22b 2b 6b and 10b. Pools of 20 pineal glands were prepared at each time point and total RNA was extracted using the RNeasy Lipid Tissue Mini Kit QIAGEN according to the manufacturer's instructions. Illumina TruSeq protocol was used to prepare libraries from RNA samples. Overall 12 libraries 12 time points were run on 2 lanes of Illumina HiSeq2000 machine using the multiplexing strategy of the TruSeq protocol Institute of Applied Genomics. On average 30 million paired end reads were obtained for each library. The reads were 2 x 100 base pairs for 8 time points CTs 22 2 6 10 18b 2b 6b 10b and 2 x 50 base pairs for the remaining time points CTs 14 18 14b and 22b.", "Zebrafish pineal gland", "Pineal gland", null, null, null, null, null, null, null, null, null, null, "Zebrafish pineal gland CT10", "Pineal gland CT10", "1", "library construction was conducted using Illumina's TruSeq RNA Sample Prep Kit following the manufacture protocol. Briefly starting from total RNA the messenger RNA was purified using polyA selection then chemically fragmented and converted into single stranded cDNA using random hexamer priming. postwards the second strand was generated to create double stranded cDNA. Finally adapters were added by ligation to the double stranded cDNA which prepared the samples for cluster generation. post library quality check by Bioanalyzer High Sensitivity chip clusters were generated and libraries were run on HiSeq2000 by using standard Illumina sequencing workflow with the multiplexing option. The mRNA libraries from the zebrafish pineal glands were sequenced on two lanes of Illumina HiSeq2000 instrument following the manufacture protocol. In each sequencing lane six bar codes were used one for each tested sample. Primary data analyses of sequence data and quality controls were performed using the Illumina pipeline version 1.7. The reads were filtered using Illumina's HiSeq2000 softwares Illumina indexes separation was also performed.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "2020Application ReadForward11Application ReadReverse102", "SRP016132", null, null, "6_zebrapg_GCCAAT_L001_R1.fastq", "fastq", 2264856522.0, 11212161.0, "Pineal gland CT10 run", "0:101 1:101", "A:618511903;C:514367008;G:514553380;T:612826453;N:4597778", 101, 101, null, null, 618511903, 514367008, 514553380, 612826453, 4597778, "SRX195410", "SRS369337", "SRA054264", "Tel Aviv University", "Tel Aviv University", 2, 0.9147, 0.91201, 0.14139, 0.14232, 0.66892, 0.67225, 0.46449, 0.46385, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "Israel", "2012-12-14", "Adult", "Adult", "Pineal Gland", "Endocrine 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": ["36573"], "units": {}, "query_ms": 8.096759003819898}