{"database": "metadata", "table": "run_metadata", "rows": [[66834, "SRR16674683", "SRX12875364", "SRS10818488", "SRP343978", "PRJNA776712", "RNA seq analysis of nde1 mutant zebrafish", "PRJNA776712", "Other", "We perform RNA sequencing to detect defferential expressed genes of nde1 deficiency mutant zebrafish brains compared to wild type.", null, null, null, null, "brain WT", null, "strain:TU|dev stage:2mpf|sex:male|tissue:brain|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio brain", "B7", "B7", "RNA seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina San Diego  CA using 5g of total RNA. Shortly  messenger RNA was isolated according to polyA selection method by oligodT beads and then fragmented by fragmentation buffer firstly. Secondly double stranded cDNA was synthesized using a SuperScript double stranded cDNA synthesis kit Invitrogen  CA with random hexamer primers Illumina.  Then the synthesized cDNA was subjected to end repair  phosphorylation and A base addition according to Illuminas library construction protocol. Libraries were size selected for cDNA target fragments of 200300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase NEB for 15 PCR cycles. post quantified by TBS380  paired end RNA seq sequencing library was sequenced with the Illumina HiSeq 4000 2  150bp read length.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "RT-PCR", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP343978", null, null, "B7.R1.fastq.gz B7.R2.fastq.gz", "fastq fastq", 6685388496.0, 22137048.0, "B7.R1.fastq.gz", "0:151 1:151", "A:1860264075;C:1483831512;G:1503216220;T:1838014556;N:62133", 151, 151, null, null, 1860264075, 1483831512, 1503216220, 1838014556, 62133, "SRX12875364", "SRS10818488", null, null, "Children's Hospital of Fudan University", 2, 0.94254, 0.93341, 0.13834, 0.13689, 0.69355, 0.69755, 0.49201, 0.49217, 151, 151, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2021-11-01", "Juvenile", "Juvenile", "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": ["66834"], "units": {}, "query_ms": 8.04404099471867}