{"database": "metadata", "table": "run_metadata", "rows": [[36685, "SRR801688", "SRX258168", "SRS406299", "SRP020469", "PRJNA195909", "RNA sequencing project for zebrafish embryo and larva development", "GSE45706", "Transcriptome Analysis", "Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. recent yrs have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes  yet large gaps still remain in the functional pathways critical for each developmental stage  especially for the late embryonic development. We sequenced the polyA extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development. Overall design: Analysis of total mRNA by highthroughput sequencing in 9 stages covering 7 periods during the embryonic and larval development of zebrafish", null, "pubmed:23700457;pubmed:26891128", "source: Zebrafish 1 wpf larvae", "GSM1112163: larva  1 week", "GSM1112163", null, "strain:AB|developmental stage:larva  1 week|tissue:larva", "larva  1 week", "Primary processing by SOLiD 3.0 online software The short SOLiD reads were aligned against the zebrafish genome build Zv9 using the software package Bioscope v1.2 obtained from Life Techlogies. Reads per kilobase of transcript per million mapped reads RPKM were calculated using an in house developed perl script  which is available upon request. Genome build: Zv9 Supplementary files format and content: tab delimited text files including RPKM values for gene models from the genome annotation release Ensembl 62 of the Zv9 assembly", "Zebrafish 1 wpf larvae", "Liquid nitrogen rapid cooling methods were used for zebrafish embryos and larvae euthanasia.", "Total RNA was extracted from each stage of about 2000 embryos or larvae using Trizol Invitrogen Carlsbad  CA  USA methods according to the manufacturer\u2019s instruction. RNA quality was evaluated by gel electrophoresis  and the concentration was measured with NanoDrop 2000 Thermo Scientific\uff0cWaltham  MA USA.The aliquots were stored at  80 oC. A protocol/kit available from Life Technologies with minor modifications was used to construct mRNA seq libraries. First  the total RNA was estimated on an Agilent 2100 Bioanalyzer Agilent Technologies Waldbronn Germany. Second  The ribosomal RNA removal steps were replaced by two rounds of polyA purification  with the first round using the PolyATtract\u00ae mRNA Isolation Systems Promega  Madison  WI  USA and the second round using the PolyAPurist\u2122 Kit Ambion  Austin  TX  USA. About 0.8 \u03bcg of mRNA was fragmented with 10min at 37 oC RNase III treatment. The fragmented mRNA were ligated with adaptor Mix A  subsequently used for reverse transcription. The first strand cDNA were separated using 6% TBE Urea Gel Invitrogen  Carlsbad  CA  USA and 100\u2013200 nt fraction was recovered. The fractionated cDNA were subjected to 11 15 cycles of PCR amplification  with the PCR products purified to yield the SOLiD Fragment Library ready for emulsion PCR. Emulsion PCR was performed using 600 pg of the library. All experiments were performed on full sequencing slides.", "Zebrafish embryos and larvae were collected and maintained at approximately 28.5\u00b0C  and were staged according to their morphological features and hours h or days dpf as described previously Kimmel et al. 1995", "strain:AB|developmental stage:larva  1 week|tissue:larva", "GSM1112163", "GSM1112163: larva  1 week; Danio rerio; RNA Seq", "GSM1112163 1", null, "1", null, "GEO Accession:GSM1112163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", null, "SRP020469", null, null, "D_rerio_1week_F3.csfasta.bz2 D_rerio_1week_F3_QV.qual.bz2", "SOLiD_native SOLiD_native", 18866346300.0, 377326926.0, "GSM1112163 r1", "0:50", "0:4319577052;1:5210931849;2:5202393345;3:4013865803;.:119578251", 50, null, null, null, null, null, null, null, null, "SRX258168", "SRS406299", "SRA072427", "GEO", "Shanghai Chenshan Botanical Garden", 1, 0.60649, null, 0.05524, null, 0.86746, null, 0.51092, null, 50, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2013-04-02", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"]], "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": ["36685"], "units": {}, "query_ms": 9.932238001056248}