{"database": "metadata", "table": "run_metadata", "rows": [[38302, "SRR1695730", "SRX798420", "SRS781712", "SRP050879", "PRJNA269540", "zebrafish transciptsome sequencing", "PRJNA269540", "Other", "we aimed to calculate the expression level of some special genes", null, null, null, "Testis from Danio rerio", "testis of zebrafish", null, "strain:AB|dev stage:adult|sex:male|tissue:testis|biomaterial provider:zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish testis", "testis of zebrafish", "Zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences", "Wild type zebrafish from an AB background were maintained in the zebrafish facilities of the Institute of Hydrobiology  Chinese Academy of Sciences. Testis of adult is collected for RNA extraction. Total RNA extraction was performed with TRIZOL reagents from Takara following the manufacturer\u2019s instructions. Total RNA contents were measured using the NanoDrop 2000. Then 5 \u03bcg total RNA was used for mRNA isolation with oligo dT magnetic beads and fragmented into small pieces in fragmentation buffer at 70\u00b0C for 4 min before cDNA synthesis. First strand cDNA was synthesized from the cleaved RNA using SuperScript II reverse transcriptase and random hexamer primers  followed by second strand cDNA synthesis using DNA polymerase I and RNaseH. post purification with a QIAquick PCR Purification Kit Qiagen  Dusseldorf  Germany  the double stranded cDNA was treated to repair ends by T4 DNA polymerase  Klenow enzyme  and T4 polynucleotide kinase NEB. This was followed by addition of a single A base using Klenow exo polymerase and ligation with an adapter using DNA ligase NEB. post ligation  the DNA was purified using a QIAquick PCR Purification Kit. PCR amplification with 10 to 12 cycles was performed with primers complementary to the adapter sequences to enrich the samples for the desired fragments. post purification using a QIAquick PCR Purification Kit  the product was dissolved in 30 \u00b5L of Qiagen EB buffer. These DNA fragments represented the designated mRNA library. The cDNA library was quantified with Qubit Invitrogen and a cluster of the DNA fragment was amplified using bridge PCR on the surface of a flow cell chip. Multiplexed libraries were sequenced for 101bp at both ends using an Illumina HiSeqTM 2000 platform.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>202</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>102</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP050879", null, null, "Zebrafish_256-T14-VI_good_1.fq.gz Zebrafish_256-T14-VI_good_2.fq.gz", "fastq fastq", 5252571430.0, 26005174.0, "testis of zebrafish", "0:100.99 1:100.99", "A:1353125230;C:1273042497;G:1273793183;T:1350916239;N:1694281", 100, 100, null, null, 1353125230, 1273042497, 1273793183, 1350916239, 1694281, "SRX798420", "SRS781712", "SRA210676", "CAS|systematic evolution", "Institute of Hydrobiology, Chinese Academy of sciences", 2, 0.93036, 0.93332, 0.09196, 0.09372, 0.64559, 0.64806, 0.48865, 0.48746, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-09-23", "Adult", "Adult", "Gonad", "Reproductive 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": ["38302"], "units": {}, "query_ms": 8.738364999999249}