{"database": "metadata", "table": "run_metadata", "rows": [[39757, "SRR2125735", "SRX1117104", "SRS1010314", "SRP061528", "PRJNA290839", "Danio rerio Transcriptome or Gene expression", "PRJNA290839", "Transcriptome Analysis", "RNA Seq of Danio rerio transcriptome", null, null, null, null, "polr1cKO", null, "breed:not applicable|strain:not applicable|age:5 dpf provider:not applicable|sex:not collected|tissue:whole fish of polr1cKO|treatment:KO|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of polr1cKO", "RNA Seq of polr1cKO", "1", "Total RNA was extracted from the cells using the mirVanaTM isolation kit Applied Biosystems and treated with DNase Ambion to remove contaminating genomic DNA. Agilent 2100 Bioanalyzer system was used to assess RNA quality of samples and the samples with a RNA Integrity Number RIN greater than 9 were used for transcriptome library construction. cDNA library wasconstructed using TruSeq Stranded Total RNA LT Sample Prep Kit Illumina  each prepared from 300ng of total RNA. The cDNA libraries were constructed according to manufacturer\u2019s instruction and index codes were ligated as identification to individual samples as previous described. Briefly  mRNA was purified from the total RNA using poly T oligo  attached magnetic beads Illumina  San Diego  USA to remove the ribosomal RNA. Then the Mrna was fragmented by using divalent cations in Illumina proprietary fragmentation buffer at 94 ?C for 1 min. First strand cDNAs were synthesized using random oligonucleotides and SuperScript II  then and second cDNAs were synthesized using DNA polymerase I and RNase H. Overhangs were blunted by using exonuclease/polymerase  followed by 3\u2019 end adenylation. post adenylation of 3\u2019 ends of DNA fragments  Illumina PE adapter oligonucleotides were ligated to DNA fragments. DNA fragments that ligated with adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycles PCR reaction. Libraries were purified using AMPure XP system and quantified using the KAPA Library Quantification Kits. Before submitted to sequencing  the libraries were normalized and pooled together in a single lane on an Illumina MiSeq platform and 150 bp paired end reads were generated.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RANDOM", "PAIRED", "ILLUMINA", "Illumina MiSeq", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>302</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>152</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP061528", null, null, "polr1cKO_S2_L001_R2_001.fastq.gz polr1cKO_S2_L001_R1_001.fastq.gz", "fastq fastq", 2153644339.0, 7160972.0, "RNA Seq of polr1cKO", "0:150.40 1:150.34", "A:558724957;C:517375772;G:514543839;T:562990605;N:9166", 150, 150, null, null, 558724957, 517375772, 514543839, 562990605, 9166, "SRX1117104", "SRS1010314", "SRA279862", "The Chinese University of Hong Kong", "The Chinese University of Hong Kong", 2, 0.95998, 0.9611, 0.07455, 0.0729, 0.65354, 0.65496, 0.45853, 0.46158, 151, 151, "B", "B", "biological fallback assumption", "illumina", "miseq", "unknown", "random_priming", "trueseq", "bulk", "bulk", "bulk", null, "China", "2015-07-24", "Larval", "Larval", "Whole Organism", "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": ["39757"], "units": {}, "query_ms": 8.477502000459936}