{"database": "metadata", "table": "run_metadata", "rows": [[38118, "SRR1551797", "SRX681417", "SRS685080", "SRP045504", "PRJNA258223", "Danio rerio strain:TL Transcriptome or Gene expression", "PRJNA258223", "Other", "Transcriptome profiling of keratocytes derived from 2dpf and 4dpf embryos", null, null, null, "keratocytes from 4dpf embryos", "keratocytes from 4dpf embryos", null, "breed:TL|strain:TL|age:4dpf|biomaterial provider:Julie Theriot  Stanford University|sex:not collected|tissue:keratocytes skin|cell type:keratocyte|dev stage:4dpf|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "4dpf keratocyte transcriptome  replicate 1", "4dpf 1", "4dpf 1", "RNA was extracted from approximately 1 x 105 keratocytes per sample using Trizol Invitrogen.  Three biological replicates were collected for each developmental stage.  Ribosomal RNA was depleted using the Ribo Zero magnetic kit Epicentre.  The remaining mRNA was then fragmented with 8 minutes incubation in 50mM sodium carbonate/bicarbonate  1mM EDTA  pH 9.2 at 95 degrees.  To prepare cDNA  first strand synthesis was performed with Superscript III Invitrogen using random hexamer priming  and second strand synthesis was performed with DNA Polymerase I NEB.  Illumina libraries were prepared from the cDNA in an automated fashion using the Illumina TruSeq sample prep kit with TruSeq adapters on a SPRIworks System I Beckman Coulter.  Sequencing reactions were performed on an Illumina Genome Analyzer IIX according to manufacturer\u2019s instructions to generate 40nt single ended reads.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>47</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP045504", null, null, "lane7_1_4dpf.fastq", "fastq", 762138229.0, 16215707.0, "4dpf 1", "0:47", "A:183899711;C:180347476;G:190086042;T:189460942;N:18344058", 47, null, null, null, 183899711, 180347476, 190086042, 189460942, 18344058, "SRX681417", "SRS685080", "SRA179326", "Stanford University|Julie Theriot", "Stanford University", 1, 0.85884, null, 0.2135, null, 0.80077, null, 0.50539, null, 47, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2014-08-15", "Larval", "Larval", "Skin", "Surface Structure"]], "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": ["38118"], "units": {}, "query_ms": 10.165034007513896}